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

How Many Cooks Spoil the Soup?

In this work, we study the following basic question: "How much parallelism does a distributed task permit?" Our definition of parallelism (or symmetry) here is not in terms of speed, but in terms of identical roles that processes have at the same time in the execution. We initiate this study in population protocols, a very simple model that not only allows for a straightforward definition of what a role is, but also encloses the challenge of isolating the properties that are due to the protocol from those that are due to the adversary scheduler, who controls the interactions between the processes. We (i) give a partial characterization of the set of predicates on input assignments that can be stably computed with maximum symmetry, i.e., $\Theta(N_{min})$, where $N_{min}$ is the minimum multiplicity of a state in the initial configuration, and (ii) we turn our attention to the remaining predicates and prove a strong impossibility result for the parity predicate: the inherent symmetry of any protocol that stably computes it is upper bounded by a constant that depends on the size of the protocol.Comment: 19 page

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

Characterization of Bovine Osteoclasts on an Ionomeric Cement In Vitro

Primary bovine osteoclasts were obtained by an outgrowth method from bovine periosteum and cultured for 7 days on an ionomeric cement for biomaterial testing. Osteoclasts cultured on slices of bovine bone and on glass microscope cover-slides served as a control. The cells were characterised as osteoclasts by a number of tests. Osteoclasts showed positive staining for tartrate resistant acid phosphatase and reactivity with the antibodies 13C2 and 23C6, which react with the alphachain of the vitronectin receptor. Addition of salmon calcitonin to the culture medium led to sudden cessation of lamellipodial activity. The cells resorbed bone by making pits. In mixed cultures with osteoblasts, the morphology of the osteoclasts on the smooth ionomeric cement surface was comparable to the one on glass cover-slides, revealing broad cytoplasmatic extensions on the material. Acridine orange staining demonstrated viability of cells until the end of the culture period and increased acidification after parathyroid hormone (PTH) stimulation. Scanning electron microscopy did not reveal erosion of the material by osteoclasts. No signs of aluminium toxicity on osteoclasts could be detected during the 7 day culture period, although an increased uptake of aluminium into the cell was demonstrated

Signal Transmission Across Tile Assemblies: 3D Static Tiles Simulate Active Self-Assembly by 2D Signal-Passing Tiles

The 2-Handed Assembly Model (2HAM) is a tile-based self-assembly model in which, typically beginning from single tiles, arbitrarily large aggregations of static tiles combine in pairs to form structures. The Signal-passing Tile Assembly Model (STAM) is an extension of the 2HAM in which the tiles are dynamically changing components which are able to alter their binding domains as they bind together. For our first result, we demonstrate useful techniques and transformations for converting an arbitrarily complex STAM$^+$ tile set into an STAM$^+$ tile set where every tile has a constant, low amount of complexity, in terms of the number and types of ``signals'' they can send, with a trade off in scale factor. Using these simplifications, we prove that for each temperature $\tau>1$ there exists a 3D tile set in the 2HAM which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $\tau$ (where the STAM$^+$ does not make use of the STAM's power of glue deactivation and assembly breaking, as the tile components of the 2HAM are static and unable to change or break bonds). This means that there is a single tile set $U$ in the 3D 2HAM which can, for an arbitrarily complex STAM$^+$ system $S$, be configured with a single input configuration which causes $U$ to exactly simulate $S$ at a scale factor dependent upon $S$. Furthermore, this simulation uses only two planes of the third dimension. This implies that there exists a 3D tile set at temperature $2$ in the 2HAM which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $1$. Moreover, we show that for each temperature $\tau>1$ there exists an STAM$^+$ tile set which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $\tau$, including the case where $\tau = 1$.Comment: A condensed version of this paper will appear in a special issue of Natural Computing for papers from DNA 19. This full version contains proofs not seen in the published versio

Density Matrix Renormalization Group Study of the S=1/2 Anisotropic Antiferromagnetic Heisenberg Chains with Quasiperiodic Exchange Modulation

The low energy behavior of the S=1/2 antiferromagnetic XY-like XXZ chains with precious mean quasiperiodic exchange modulation is studied by the density matrix renormalization group method. It is found that the energy gap of the chain with length N scales as $\exp (-cN^{\omega})$ with nonuniversal exponent $\omega$ if the Ising component of the exhange coupling is antiferromagnetic. This behavior is expected to be the characteristic feature of the quantum spin chains with relevant aperiodicity. This is in contrast to the XY chain for which the precious mean exchange modulation is marginal and the gap scales as $N^{-z}$. On the contrary, it is also verified that the energy gap scales as $N^{-1}$ if the Ising component of the exhange coupling is ferromagnetic. Our results are not only consistent with the recent bosonization analysis of Vidal, Mouhanna and Giamarchi but also clarify the nature of the strong coupling regime which is inaccesssible by the bosonization approach.Comment: 8 pages, 15 figures, 1 table; Proceedings of the workshop 'Frontiers in Magnetism', Kyoto, Oct. 199

Ground-State Phase Diagram of the Two-Dimensional Quantum Heisenberg Mattis Model

The two-dimensional $S=1/2$ asymmetric Heisenberg Mattis model is investigated with the exact diagonalization of finite clusters. The N\'eel order parameter and the spin glass order parameter can be smoothly extrapolated to the thermodynamic limit in the antiferromagnetic region, as in the pure Heisenberg antiferromagnet. The critical concentration of the N\'eel phase is consistent with that of the two-dimensional Ising Mattis model, and the spin glass order parameter increases monotonously as the ferro-bond concentration increases. These facts suggest that quantum fluctuation does not play an essential role in two-dimensional non-frustrated random spin systems. KEYWORDS: quantum spin system, ground state, randomness, Mattis model, N\'eel order, spin glass orderComment: 10 pages, LaTeX, 6 compressed/uuencoded postscript figures, J. Phys. Soc. Jpn. 65 (1996) No. 2 in pres

Bounding the dimensions of rational cohomology groups

Let $k$ be an algebraically closed field of characteristic $p > 0$, and let $G$ be a simple simply-connected algebraic group over $k$ that is defined and split over the prime field $\mathbb{F}_p$. In this paper we investigate situations where the dimension of a rational cohomology group for $G$ can be bounded by a constant times the dimension of the coefficient module. We then demonstrate how our results can be applied to obtain effective bounds on the first cohomology of the symmetric group. We also show how, for finite Chevalley groups, our methods permit significant improvements over previous estimates for the dimensions of second cohomology groups.Comment: 13 page

Protocol for Future Amino Acid Analyses of Samples Returned by the Stardust Mission

We have demonstrated that LC-ToF-MS coupled with UV fluorescence detection is a powerful tool for the detection of amino acids in meteorite extracts. Using this new analytical technique we were able to identify the extraterrestrial amino acid AIB extracted from fifteen 20 micron sized Murchison meteorite grains. We found that the amino acid contamination levels in Stardust aerogels was much lower than the levels observed in the Murchison meteorite. In addition, the alpha-dialkyl amino acids AIB and isovaline which are the most abundant amino acids in Murchison were not detected in the aerogel above blank levels. We are currently integrating LIF detection capability to our existing nanoflow LC-ToF-MS for enhanced sensitivity required for the analysis of amino acids in Stardust samples

Optimal self-assembly of finite shapes at temperature 1 in 3D

Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for an arbitrary finite, connected shape $X \subset \mathbb{Z}^2$, there is a tile set that uniquely self-assembles into a 3D representation of a scaled-up version of $X$ at temperature 1 in 3D with optimal program-size complexity (the "program-size complexity", also known as "tile complexity", of a shape is the minimum number of tile types required to uniquely self-assemble it). Moreover, our construction is "just barely" 3D in the sense that it only places tiles in the $z = 0$ and $z = 1$ planes. Our result is essentially a just-barely 3D temperature 1 simulation of a similar 2D temperature 2 result by Soloveichik and Winfree (SICOMP 2007)