Verification in Staged Tile Self-Assembly

We prove the unique assembly and unique shape verification problems, benchmark measures of self-assembly model power, are $\mathrm{coNP}^{\mathrm{NP}}$-hard and contained in $\mathrm{PSPACE}$ (and in $\mathrm{\Pi}^\mathrm{P}_{2s}$ for staged systems with $s$ stages). En route, we prove that unique shape verification problem in the 2HAM is $\mathrm{coNP}^{\mathrm{NP}}$-complete.Comment: An abstract version will appear in the proceedings of UCNC 201

Covert Computation in Staged Self-Assembly: Verification Is PSPACE-Complete

Staged self-assembly has proven to be a powerful abstract model of self-assembly by modeling laboratory techniques where several nanoscale systems are allowed to assemble separately and then be mixed at a later stage. A fundamental problem in self-assembly is Unique Assembly Verification (UAV), which asks whether a single final assembly is uniquely constructed. This has previously been shown to be ?^{p}?-hard in staged self-assembly with a constant number of stages, but a more precise complexity classification was left open related to the polynomial hierarchy. Covert Computation was recently introduced as a way to compute a function while hiding the input to that function for self-assembly systems. These Tile Assembly Computers (TACs), in a growth only negative aTAM system, can compute arbitrary circuits, which proves UAV is coNP-hard in that model. Here, we show that the staged assembly model is capable of covert computation using only 3 stages. We then utilize this construction to show UAV with only 3 stages is ?^{p}?-hard. We then extend this technique to open problems and prove that general staged UAV is PSPACE-complete. Measuring the complexity of n stage UAV, we show ?^{p}_{n - 1}-hardness. We finish by showing a ?^{p}_{n + 1} algorithm to solve n stage UAV leaving only a constant gap between membership and hardness

Verification in Generalizations of the 2-Handed Assembly Model

Algorithmic Self Assembly is a well studied field in theoretical computer science motivated by the analogous real world phenomenon of DNA self assembly, as well as the emergence of nanoscale technology. Abstract mathematical models of self assembly such as the Two Handed Assembly model (2HAM) allow us to formally study the computational capabilities of self assembly. The 2HAM is one of the most thoroughly studied models of self assembly, and thus in this paper we study generalizations of this model. The Staged Tile Assembly model captures the behavior of being able to separate assembly processes and combine their outputs at a later time. The k-Handed Assembly Model relaxes the restriction of the 2HAM that only two assemblies can combine in one assembly step. The 2HAM with prebuilt assemblies considers the idea that you can start your assembly process with some prebuilt structures. These generalizations relax some rules of the 2HAM, in ways which reflect real world self assembly mechanics and capabilities. We investigate the complexity of verification problems in these new models, such as the problem of verifying whether a system produces a specified assembly (Producibility), and verifying whether a system uniquely assembles a specified assembly (Unique Assembly Verification). We show that these generalizations introduce a high amount of intractability to these verification problems

Computational Complexity in Tile Self-Assembly

One of the most fundamental and well-studied problems in Tile Self-Assembly is the Unique Assembly Verification (UAV) problem. This algorithmic problem asks whether a given tile system uniquely assembles a specific assembly. The complexity of this problem in the 2-Handed Assembly Model (2HAM) at a constant temperature is a long-standing open problem since the model was introduced. Previously, only membership in the class coNP was known and that the problem is in P if the temperature is one (τ = 1). The problem is known to be hard for many generalizations of the model, such as allowing one step into the third dimension or allowing the temperature of the system to be a variable, but the most fundamental version has remained open. In this Thesis I will cover verification problems in different models of self-assembly leading to the proof that the UAV problem in the 2HAM is hard even with a small constant temperature (τ = 2), and finally answer the complexity of this problem (open since 2013). Further, this result proves that UAV in the staged self-assembly model is coNP-complete with a single bin and stage (open since 2007), and that UAV in the q-tile model is also coNP-complete (open since 2004). We reduce from Monotone Planar 3-SAT with Neighboring Variable Pairs, a special case of 3SAT recently proven to be NP-hard

Unique Assembly Verification in Two-Handed Self-Assembly

One of the most fundamental and well-studied problems in Tile Self-Assembly is the Unique Assembly Verification (UAV) problem. This algorithmic problem asks whether a given tile system uniquely assembles a specific assembly. The complexity of this problem in the 2-Handed Assembly Model (2HAM) at a constant temperature is a long-standing open problem since the model was introduced. Previously, only membership in the class coNP was known and that the problem is in P if the temperature is one (τ=1). The problem is known to be hard for many generalizations of the model, such as allowing one step into the third dimension or allowing the temperature of the system to be a variable, but the most fundamental version has remained open.In this paper, we prove the UAV problem in the 2HAM is hard even with a small constant temperature (τ=2), and finally answer the complexity of this problem (open since 2013). Further, this result proves that UAV in the staged self-assembly model is coNP-complete with a single bin and stage (open since 2007), and that UAV in the q-tile model is also coNP-complete (open since 2004). We reduce from Monotone Planar 3-SAT with Neighboring Variable Pairs, a special case of 3SAT recently proven to be NP-hard. We accompany this reduction with a positive result showing that UAV is solvable in polynomial time with the promise that the given target assembly will have a tree-shaped bond graph, i.e., contains no cycles. We provide a O(n5) algorithm for UAV on tree-bonded assemblies when the temperature is fixed to 2, and a O(n5logτ) time algorithm when the temperature is part of the input

Verification and Computation in Restricted Tile Automata

Many models of self-assembly have been shown to be capable of performing computation. Tile Automata was recently introduced combining features of both Celluar Automata and the 2-Handed Model of self-assembly both capable of universal computation. In this work we study the complexity of Tile Automata utilizing features inherited from the two models mentioned above. We first present a construction for simulating Turing Machines that performs both covert and fuel efficient computation. We then explore the capabilities of limited Tile Automata systems such as 1-Dimensional systems (all assemblies are of height 1) and freezing Systems (tiles may not repeat states). Using these results we provide a connection between the problem of finding the largest uniquely producible assembly using n states and the busy beaver problem for non-freezing systems and provide a freezing system capable of uniquely assembling an assembly whose length is exponential in the number of states of the system. We finish by exploring the complexity of the Unique Assembly Verification problem in Tile Automata with different limitations such as freezing and systems without the power of detachment

Verification and Computation in Restricted Tile Automata

Many models of self-assembly have been shown to be capable of performing computation. Tile Automata was recently introduced combining features of both Celluar Automata and the 2-Handed Model of self-assembly both capable of universal computation. In this work we study the complexity of Tile Automata utilizing features inherited from the two models mentioned above. We first present a construction for simulating Turing Machines that performs both covert and fuel efficient computation. We then explore the capabilities of limited Tile Automata systems such as 1-Dimensional systems (all assemblies are of height 1) and freezing Systems (tiles may not repeat states). Using these results we provide a connection between the problem of finding the largest uniquely producible assembly using n states and the busy beaver problem for non-freezing systems and provide a freezing system capable of uniquely assembling an assembly whose length is exponential in the number of states of the system. We finish by exploring the complexity of the Unique Assembly Verification problem in Tile Automata with different limitations such as freezing and systems without the power of detachment

Covert Computation in the Abstract Tile-Assembly Model

There have been many advances in molecular computation that offer benefits such as targeted drug delivery, nanoscale mapping, and improved classification of nanoscale organisms. This power led to recent work exploring privacy in the computation, specifically, covert computation in self-assembling circuits. Here, we prove several important results related to the concept of a hidden computation in the most well-known model of self-assembly, the Abstract Tile-Assembly Model (aTAM). We show that in 2D, surprisingly, the model is capable of covert computation, but only with an exponential-sized assembly. We also show that the model is capable of covert computation with polynomial-sized assemblies with only one step in the third dimension (just-barely 3D). Finally, we investigate types of functions that can be covertly computed as members of P/Poly