Related papers: The tile assembly model is intrinsically universal
The Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of…
We show that in the hierarchical tile assembly model, if there is a producible assembly that overlaps a nontrivial translation of itself consistently (i.e., the pattern of tile types in the overlap region is identical in both translations),…
Tile-based self-assembly systems are capable of universal computation and algorithmically-directed growth. Systems capable of such behavior typically make use of "glue cooperation" in which the glues on at least $2$ sides of a tile must…
Behaviors of Winfree's tile assembly systems (TASs) at high temperatures are investigated in combination with integer programming of a specific form called threshold programming. First, we propose a way to build bridges from the Boolean…
The recently introduced Thermodynamic Binding Networks (TBN) model was developed with the purpose of studying self-assembling systems by focusing on their thermodynamically favorable final states, and ignoring the kinetic pathways through…
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…
Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the…
The emerging field of passive macro-scale tile-based self-assembly (TBSA) shows promise in enabling effective manufacturing processes by harnessing TBSA's intrinsic parallelism. However, current TBSA methodologies still do not fulfill their…
Working in Winfree's abstract tile assembly model, we show that a constant-size tile assembly system can be programmed through relative tile concentrations to build an n x n square with high probability, for any sufficiently large n. This…
Self-assembly plays an essential role in many natural processes, involving the formation and evolution of living or non-living structures, and shows potential applications in many emerging domains. In existing research and practice, there…
This paper presents the implementation of a self-replicating finite-state machine (FSM) and a self-replicating Turing Machine (TM) using bio-inspired mechanisms. Building on previous work that introduced self-replicating structures capable…
This work establishes a rigorous theoretical foundation for analyzing deep learning systems by leveraging Infinite Time Turing Machines (ITTMs), which extend classical computation into transfinite ordinal steps. Using ITTMs, we reinterpret…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
We introduce a toy model of ecosystem assembly for which we are able to map out all assembly pathways generated by external invasions. The model allows to display the whole phase space in the form of an assembly graph whose nodes are…
Majumder, Reif and Sahu have presented a stochastic model of reversible, error-permitting, two-dimensional tile self-assembly, and showed that restricted classes of tile assembly systems achieved equilibrium in (expected) polynomial time.…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…
Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions…
The design of irregular planar phased arrays (PAs) characterized by a highly-modular architecture is addressed. By exploiting the property of self-replicating tile shapes, also known as rep-tiles, the arising array layouts consist of tiles…
We advance a Bayesian concept of 'intrinsic asymptotic universality' taking to its final conclusions previous conceptual and numerical work based upon a concept of a reprogrammability test and an investigation of the complex qualitative…
We show here that a model called directed self-assembly at temperature 1 is unable to do complex computations like the ones of a Turing machine. Since this model can be seen as a generalization of finite automata to 2D languages, a logical…