arXiv subjects

Robert Schweller

Publications and source records attributed to Robert Schweller.

25 records · Page 2Linked to original sources

arXiv2016

Concentration Independent Random Number Generation in Tile Self-Assembly

In this paper we introduce the \emph{robust random number generation} problem where the goal is to design an abstract tile assembly system (aTAM system) whose terminal assemblies can be split into $n$ partitions such that a resulting assembly of the system lies within each partition with probability 1/$n$, regardless of the relative concentration assignment of the tile types in the system. First, we show this is possible for $n=2$ (a \emph{robust fair coin flip}) within the aTAM, and that such systems guarantee a worst case $\mathcal{O}(1)$ space usage. We accompany our primary construction with variants that show trade-offs in space complexity, initial seed size, temperature, tile complexity, bias, and extensibility, and also prove some negative results. As an application, we combine our coin-flip system with a result of Chandran, Gopalkrishnan, and Reif to show that for any positive integer $n$, there exists a $\mathcal{O}(\log n)$ tile system that assembles a constant-width linear assembly of expected length $n$ for any concentration assignment. We then extend our robust fair coin flip result to solve the problem of robust random number generation in the aTAM for all $n$. Two variants of robust random bit generation solutions are presented: an unbounded space solution and a bounded space solution which incurs a small bias. Further, we consider the harder scenario where tile concentrations change arbitrarily at each assembly step and show that while this is not possible in the aTAM, the problem can be solved by exotic tile assembly models from the literature.

cs.FL↗

arXiv2013

Fast Arithmetic in Algorithmic Self-Assembly

In this paper we consider the time complexity of computing the sum and product of two $n$-bit numbers within the tile self-assembly model. The (abstract) tile assembly model is a mathematical model of self-assembly in which system components are square tiles with different glue types assigned to tile edges. Assembly is driven by the attachment of singleton tiles to a growing seed assembly when the net force of glue attraction for a tile exceeds some fixed threshold. Within this frame work, we examine the time complexity of computing the sum or product of 2 n-bit numbers, where the input numbers are encoded in an initial seed assembly, and the output is encoded in the final, terminal assembly of the system. We show that the problems of addition and multiplication have worst case lower bounds of $Ω(\sqrt{n})$ in 2D assembly, and $Ω(\sqrt[3]{n})$ in 3D assembly. In the case of addition, we design algorithms for both 2D and 3D that meet this bound with worst case run times of $O(\sqrt{n})$ and $O(\sqrt[3]{n})$ respectively, which beats the previous best known upper bound of O(n). Further, we consider average case complexity of addition over uniformly distributed n-bit strings and show how to achieve $O(\log n)$ average case time with a simultaneous $O(\sqrt{n})$ worst case run time in 2D. For multiplication, we present an $O(n^{5/6})$ time multiplication algorithm which works in 3D, which beats the previous best known upper bound of O(n). As additional evidence for the speed of our algorithms, we implement our addition algorithms, along with the simpler O(n) time addition algorithm, into a probabilistic run-time simulator and compare the timing results.

cs.DS↗

arXiv2012

Fuel Efficient Computation in Passive Self-Assembly

In this paper we show that passive self-assembly in the context of the tile self-assembly model is capable of performing fuel efficient, universal computation. The tile self-assembly model is a premiere model of self-assembly in which particles are modeled by four-sided squares with glue types assigned to each tile edge. The assembly process is driven by positive and negative force interactions between glue types, allowing for tile assemblies floating in the plane to combine and break apart over time. We refer to this type of assembly model as passive in that the constituent parts remain unchanged throughout the assembly process regardless of their interactions. A computationally universal system is said to be fuel efficient if the number of tiles used up per computation step is bounded by a constant. Work within this model has shown how fuel guzzling tile systems can perform universal computation with only positive strength glue interactions. Recent work has introduced space-efficient, fuel-guzzling universal computation with the addition of negative glue interactions and the use of a powerful non-diagonal class of glue interactions. Other recent work has shown how to achieve fuel efficient computation within active tile self-assembly. In this paper we utilize negative interactions in the tile self-assembly model to achieve the first computationally universal passive tile self-assembly system that is both space and fuel-efficient. In addition, we achieve this result using a limited diagonal class of glue interactions.

cs.DS↗

arXiv2012

Two Hands Are Better Than One (up to constant factors)

We study the difference between the standard seeded model of tile self-assembly, and the "seedless" two-handed model of tile self-assembly. Most of our results suggest that the two-handed model is more powerful. In particular, we show how to simulate any seeded system with a two-handed system that is essentially just a constant factor larger. We exhibit finite shapes with a busy-beaver separation in the number of distinct tiles required by seeded versus two-handed, and exhibit an infinite shape that can be constructed two-handed but not seeded. Finally, we show that verifying whether a given system uniquely assembles a desired supertile is co-NP-complete in the two-handed model, while it was known to be polynomially solvable in the seeded model.

cs.CC↗

arXiv2010

Algorithms for Testing Monomials in Multivariate Polynomials

This paper is our second step towards developing a theory of testing monomials in multivariate polynomials. The central question is to ask whether a polynomial represented by an arithmetic circuit has some types of monomials in its sum-product expansion. The complexity aspects of this problem and its variants have been investigated in our first paper by Chen and Fu (2010), laying a foundation for further study. In this paper, we present two pairs of algorithms. First, we prove that there is a randomized $O^*(p^k)$ time algorithm for testing $p$-monomials in an $n$-variate polynomial of degree $k$ represented by an arithmetic circuit, while a deterministic $O^*(6.4^k + p^k)$ time algorithm is devised when the circuit is a formula, here $p$ is a given prime number. Second, we present a deterministic $O^*(2^k)$ time algorithm for testing multilinear monomials in $Π_mΣ_2Π_t\times Π_kΠ_3$ polynomials, while a randomized $O^*(1.5^k)$ algorithm is given for these polynomials. The first algorithm extends the recent work by Koutis (2008) and Williams (2009) on testing multilinear monomials. Group algebra is exploited in the algorithm designs, in corporation with the randomized polynomial identity testing over a finite field by Agrawal and Biswas (2003), the deterministic noncommunicative polynomial identity testing by Raz and Shpilka (2005) and the perfect hashing functions by Chen {\em at el.} (2007). Finally, we prove that testing some special types of multilinear monomial is W[1]-hard, giving evidence that testing for specific monomials is not fixed-parameter tractable.

cs.CC↗

arXiv2006

Reducing Tile Complexity for Self-Assembly Through Temperature Programming

We consider the tile self-assembly model and how tile complexity can be eliminated by permitting the temperature of the self-assembly system to be adjusted throughout the assembly process. To do this, we propose novel techniques for designing tile sets that permit an arbitrary length $m$ binary number to be encoded into a sequence of $O(m)$ temperature changes such that the tile set uniquely assembles a supertile that precisely encodes the corresponding binary number. As an application, we show how this provides a general tile set of size O(1) that is capable of uniquely assembling essentially any $n\times n$ square, where the assembled square is determined by a temperature sequence of length $O(\log n)$ that encodes a binary description of $n$. This yields an important decrease in tile complexity from the required $Ω(\frac{\log n}{\log\log n})$ for almost all $n$ when the temperature of the system is fixed. We further show that for almost all $n$, no tile system can simultaneously achieve both $o(\log n)$ temperature complexity and $o(\frac{\log n}{\log\log n})$ tile complexity, showing that both versions of an optimal square building scheme have been discovered. This work suggests that temperature change can constitute a natural, dynamic method for providing input to self-assembly systems that is potentially superior to the current technique of designing large tile sets with specific inputs hardwired into the tileset.

cs.CC↗

arXiv2006

Randomized Fast Design of Short DNA Words

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous work has extended results from coding theory to obtain bounds on code size for new biologically motivated constraints and has applied heuristic local search and genetic algorithm techniques for code design. This paper proposes a natural optimization formulation of the DNA code design problem in which the goal is to design n strings that satisfy a given set of constraints while minimizing the length of the strings. For multiple sets of constraints, we provide high-probability algorithms that run in time polynomial in n and any given constraint parameters, and output strings of length within a constant factor of the optimal. To the best of our knowledge, this work is the first to consider this type of optimization problem in the context of DNA code design.

cs.DS↗