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

Magnetic cylindrical colloids at liquid interfaces exhibit non-volatile switching of their orientation in an external field

We study the orientation of magnetic cylindrical particles adsorbed at a liquid interface in an external field using analytical theory and high resolution finite element simulations. Cylindrical particles are interesting since they possess multiple locally stable orientations at the liquid interface so that the orientational transitions induced by an external field will not disappear when the external field is removed, i.e., the switching effect is \emph{non-volatile}. We show that, in the absence of an external field, as we reduce the aspect ratio $\alpha$ of the cylinders below a critical value ($\alpha_c \approx 2$) the particles undergo spontaneous symmetry breaking from a stable side-on state to one of two equivalent stable tilted states, similar to the spontaneous magnetisation of a ferromagnet going through the Curie point. By tuning both the aspect ratio and contact angle of the cylinders, we show that it is possible to engineer particles that have one, two, three or four locally stable orientations. We also find that the magnetic responses of cylinders with one or two stable states are similar to that of paramagnets and ferromagnets respectively, while the magnetic response of systems with three or four stable states are even more complex and have no analogs in simple magnetic systems. Magnetic cylinders at liquid interfaces therefore provide a facile method for creating switchable functional monolayers where we can use an external field to induce multiple non-volatile changes in particle orientation and self-assembled structure

Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.

The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation