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We introduce a new model of \emph{step} Chemical Reaction Networks (step CRNs), motivated by the step-wise addition of materials in standard lab procedures. Step CRNs have ordered reactants that transform into products via reaction rules over a series of steps. We study an important subset of weak reaction rules, \emph{void} rules, in which chemical species may only be deleted but never changed. We demonstrate the capabilities of these simple limited systems to simulate threshold circuits and compute functions using various configurations of rule sizes and step constructions, and prove that without steps, void rules are incapable of these computations, which further motivates the step model. Additionally, we prove the coNP-completeness of verifying if a given step CRN computes a function, holding even for $O(1)$ step systems.

We extend the motion-planning-through-gadgets framework to several new scenarios involving various numbers of robots/agents, and analyze the complexity of the resulting motion-planning problems. While past work considers just one robot or one robot per player, most of our models allow for one or more locations to spawn new robots in each time step, leading to arbitrarily many robots. In the 0-player context, where all motion is deterministically forced, we prove that deciding whether any robot ever reaches a specified location is undecidable, by representing a counter machine. In the 1-player context, where the player can choose how to move the robots, we prove equivalence to Petri nets, EXPSPACE-completeness for reaching a specified location, PSPACE-completeness for reconfiguration, and ACKERMANN-completeness for reconfiguration when robots can be destroyed in addition to spawned. Finally, we consider a variation on the standard 2-player context where, instead of one robot per player, we have one robot shared by the players, along with a ko rule to prevent immediately undoing the previous move. We prove this impartial 2-player game EXPTIME-complete., Comment: 22 pages, 19 figures. Presented at SAND 2023

We analyze the computational complexity of basic reconfiguration problems for the recently introduced surface Chemical Reaction Networks (sCRNs), where ordered pairs of adjacent species nondeterministically transform into a different ordered pair of species according to a predefined set of allowed transition rules (chemical reactions). In particular, two questions that are fundamental to the simulation of sCRNs are whether a given configuration of molecules can ever transform into another given configuration, and whether a given cell can ever contain a given species, given a set of transition rules. We show that these problems can be solved in polynomial time, are NP-complete, or are PSPACE-complete in a variety of different settings, including when adjacent species just swap instead of arbitrary transformation (swap sCRNs), and when cells can change species a limited number of times (k-burnout). Most problems turn out to be at least NP-hard except with very few distinct species (2 or 3).

We analyze Solo Chess puzzles, where the input is an $n \times n$ board containing some standard Chess pieces of the same color, and the goal is to make a sequence of capture moves to reduce down to a single piece. Prior work analyzes this puzzle for a single piece type when each piece is limited to make at most two capture moves (as in the Solo Chess puzzles on chess.com). By contrast, we study when each piece can make an unlimited number of capture moves. We show that any single piece type can be solved in polynomial time in a general model of piece types, while any two standard Chess piece types are NP-complete. We also analyze the restriction (as on chess.com) that one piece type is unique and must be the last surviving piece, showing that in this case some pairs of piece types become tractable while others remain hard., Comment: 22 pages, 9 figures. Presented at JCDCGGG 2022

The popularity of molecular computation has given rise to several models of abstraction, one of the more recent ones being Chemical Reaction Networks (CRNs). These are equivalent to other popular computational models, such as Vector Addition Systems and Petri-Nets, and restricted versions are equivalent to Population Protocols. This paper continues the work on core reachability questions related to Chemical Reaction Networks; given two configurations, can one reach the other according to the system's rules? With no restrictions, reachability was recently shown to be Ackermann-complete, this resolving a decades-old problem. Here, we fully characterize monotone reachability problems based on various restrictions such as the rule size, the number of rules that may create a species (k-source) or consume a species (k-consuming), the volume, and whether the rules have an acyclic production order (feed-forward). We show PSPACE-completeness of reachability with only bimolecular reactions with two-source and two-consuming rules. This proves hardness of reachability in Population Protocols, which was unknown. Further, this shows reachability in CRNs is PSPACE-complete with size-2 rules, which was previously only known with size-5 rules. This is achieved using techniques within the motion planning framework. We provide many important results for feed-forward CRNs where rules are single-source or single-consuming. We show that reachability is solvable in polynomial time if the system does not contain special void or autogenesis rules. We then fully characterize all systems of this type and show that if you allow void/autogenesis rules, or have more than one source and one consuming, the problems become NP-complete. Finally, we show several interesting special cases of CRNs based on these restrictions or slight relaxations and note future significant open questions related to this taxonomy., Comment: This research was supported in part by National Science Foundation Grant CCF-1817602

Tile Automata is a recently defined model of self-assembly that borrows many concepts from cellular automata to create active self-assembling systems where changes may be occurring within an assembly without requiring attachment. This model has been shown to be powerful, but many fundamental questions have yet to be explored. Here, we study the state complexity of assembling $n \times n$ squares in seeded Tile Automata systems where growth starts from a seed and tiles may attach one at a time, similar to the abstract Tile Assembly Model. We provide optimal bounds for three classes of seeded Tile Automata systems (all without detachment), which vary in the amount of complexity allowed in the transition rules. We show that, in general, seeded Tile Automata systems require $\Theta{(\log^{\frac{1}{4}} n)}$ states. For single-transition systems, where only one state may change in a transition rule, we show a bound of $\Theta{(\log^{\frac{1}{3}} n)}$, and for deterministic systems, where each pair of states may only have one associated transition rule, a bound of $\Theta( (\frac{\log n}{\log \log n})^\frac{1}{2} )$., Comment: An earlier version was published in the 2022 Symposium on Algorithmic Foundations of Dynamic Networks (SAND)

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 ($\tau=1$). 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 ($\tau = 2$), 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 $\mathcal{O}(n^5)$ algorithm for UAV on tree-bonded assemblies when the temperature is fixed to $2$, and a $\mathcal{O}(n^5\log \tau)$ time algorithm when the temperature is part of the input.

Motivated by advances is nanoscale applications and simplistic robot agents, we look at problems based on using a global signal to move all agents when given a limited number of directional signals and immovable geometry. We study a model where unit square particles move within a 2D grid based on uniform external forces. Movement is based on a sequence of uniform commands which cause all particles to move 1 step in a specific direction. The 2D grid board additionally contains "blocked" spaces which prevent particles from entry. Within this model, we investigate the complexity of deciding 1) whether a target location on the board can be occupied (by any) particle (\emph{occupancy problem}), 2) whether a specific particle can be relocated to another specific position in the board (\emph{relocation problem}), and 3) whether a board configuration can be transformed into another configuration (\emph{reconfiguration problem}). We prove that while occupancy is solvable in polynomial time, the relocation and reconfiguration problems are both NP-Complete even when restricted to only 2 or 3 movement directions. We further define a hierarchy of board geometries and show that this hardness holds for even very restricted classes of board geometry., Comment: A short abstract of this was presented at the 22nd Japan Conference on Discrete and Computational Geometry, Graphs, and Games (JCDCG3'19), 39-40, 2019

We investigate the problem of assembling general shapes and patterns in a model in which particles move based on uniform external forces until they encounter an obstacle. While previous work within this model of assembly has focused on designing a specific board configuration for the assembly of a specific given shape, we propose the problem of designing universal configurations that are capable of constructing a large class of shapes and patterns. In particular, for given integers $h,w$, we show that there exists a strongly universal configuration (no excess particles) with $\mathcal{O}(hw)$ $1 \times 1$ slidable particles that can be reconfigured to build any $h \times w$ patterned rectangle. We then expand this result to show that there exists a weakly universal configuration that can build any $h \times w$-bounded size connected shape. Following these results, we go on to show the existence of a strongly universal configuration which can assemble any shape within a previously studied ``drop'' class, while using quadratically less space than previous results. Finally, we include a study of the complexity of motion planning in this model. We consider the problems of deciding if a board location can be occupied by any particle (occupancy problem), deciding if a specific particle may be relocated to another position (relocation problem), and deciding if a given configuration of particles may be transformed into a second given configuration (reconfiguration problem). We show all of these problems to be PSPACE-complete with the allowance of a single $2\times 2$ polyomino in addition to $1\times 1$ tiles. We further show that relocation and occupancy remain PSPACE-complete even when the board geometry is a simple rectangle if domino polyominoes are included.