Abstract 1 Introduction 2 Abstract tile assembly model 3 State of the art, roadmap and main obstacles References

A Linear Bound for the Size of the Finite Terminal Assembly of a Directed Non-Cooperative Tile Assembly System

Sergiu Ivanov ORCID IBISC, Univ Évry, University of Paris-Saclay, Évry, France    Damien Regnault ORCID IBISC, Univ Évry, University of Paris-Saclay, Évry, France
Abstract

Introduced in [32], the abstract tile assembly model (aTAM) is a model of DNA self-assembly. Most of the studies focus on cooperative aTAM where a form of synchronization between the tiles is possible. Simulating Turing machines is achievable in this context. Few results and constructions are known for the non-cooperative case (a variant of Wang tilings [30] where assemblies do not need to cover the whole plane and some mismatches may occur). For example, assembly of a square of width n is done with 2n1 tiles types whereas only Θ(log(n)log(log(n))) are required for the cooperative case [2].

Introduced by P.-É. Meunier in [17], efficient paths are a non-trivial construction for non-cooperative aTAM designed with n different tile types and reaching a distance linearly greater than n. Improved in [19], efficient paths were shown to be able to reach a distance of nlog(n). Assembling them relies heavily on a form of “non-determinism”. Indeed, the set of tiles may produce different finite terminal assemblies but they all contain the same efficient path. In this paper, we prove that this non-determinism is strictly necessary for assembling the efficient paths of [19]. More formally, we show that if the terminal assembly of a directed non-cooperative tile assembly system (a model where only one terminal assembly is produced) is finite then its width and length are linear in the number of tiles. This result also implies that the construction of a square of width n using 2n1 tiles types is asymptotically optimal. Moreover, we hope that the techniques introduced here will lead to a better comprehension of the non-directed case.

Keywords and phrases:
Models of computation, DNA self-assembly, aTAM, Complexity
Category:
Track A: Algorithms, Complexity and Games
Copyright and License:
[Uncaptioned image] © Sergiu Ivanov and Damien Regnault; licensed under Creative Commons License CC-BY 4.0
2012 ACM Subject Classification:
Theory of computation Models of computation
Related Version:
Full Version: https://arxiv.org/abs/2405.18630 [14]
Acknowledgements:
We would like to thank Pierre-Étienne Meunier and Damien Woods for their helpful remarks and comments.
Funding:
The authors were partially supported by the project CalcADN (ANR-24-RRII-0001), funded by the French National Center for Scientific Research (CNRS).
Editors:
Sayan Bhattacharya, Danupon Nanongkai, Michael Benedikt, and Gabriele Puppis

1 Introduction

Modern processors align several hundred of billions of transistors on small chips. Independently, each transistor only simulates a simple Boolean function, but together they can achieve far more complex computations. Developing a formalism to describe complex mathematical functions by iterating simple building blocks originates from the seminal work by Turing on the abstract Turing machine – the very first formal model of computing. Studying both this abstract model and concrete computers derived from it became what is commonly known as computer science.

More recently, the DNA molecule emerged as a possible elementary component to carry computation instead of the conventional transistor. Indeed, Adleman [1] showed that algorithms can be implemented by mixing together cleverly designed DNA strands, creating a massively parallel model of computing. Several approaches relying on self-assembly were later implemented: in [26] Rothemund developed a technique of DNA origami to fold a long DNA strand (scaffold) using hundreds of shorter DNA strands (staples), resulting in specific shapes of size on the order of hundreds of nanometers. In [28] fractals were assembled out of DNA. In [25] artificial neural networks were simulated. In [35] cyclic machines were experimentally implemented, using DNA both as machine material and as fuel.

Over time, several possible applications have emerged. On the one hand, DNA can be an efficient way to store large amounts of information for millions of years [5]. On the other hand, DNA can be used to construct chemical seeds allowing to detect small concentrations of a target molecular compound [23]. In [31] a DNA cage was built around the hepatitis B virus to neutralize it in vitro. The crisscross slats approach in [33] allows the assembly of large structures several microns in size, opening up the possibility of interaction with biological cells.

Abstractly, some approaches to computing with DNA can be seen as a population of tiles assembling into the target structure by attaching to a seed, which represents the input. The corresponding theoretical model of computation called the abstract Tile Assembly Model (aTAM) was introduced by Winfree in [27, 32]. The aTAM relies on square tiles with glues on each of the four sides. When the glues on two tiles match, the tiles bind together forming an assembly. This assembly grows until it becomes terminal, i.e. until no more tiles can bind to it. This model can be implemented experimentally by representing tiles as small DNA complexes binding to a seed (a DNA origami) to carry out the computation, as shown in [34]. Furthermore, aTAM is able to simulate crisscross slats [9]. Lots of variants of aTAM exist, and notably cooperative aTAM (or temperature 2 aTAM) including a mechanism by which different parts of the assembly may synchronize. In this case, simulating a Turing machine is easily achieved and cooperative aTAM was shown to be intrinsically universal [7]. Due to the possible applications to DNA computing, studies also focus on the shapes which can be assembled. For example, [29] focuses on the Kolmogorov complexity of the shapes and shows a strong connection between the complexity of a shape and the number of distinct tile types necessary to assemble it. The special case of the square was studied in deep detail in [2], this shape being a kind of benchmark for computational expressiveness.

1.1 Non-cooperative aTAM

From this point on, we focus on non-cooperative aTAM. In this variant, there is no mechanism to synchronise different parts of the assembly beyond concurrency: the first path to grow blocks and prevents the growth of others. Non-cooperative aTAM can be seen as a variant of Wang tiles [30] where the computation starts from a seed and mismatches are allowed. Surprisingly, this model proved very hard to study, and very few results were known for a long time. Concerning decidability seen as the limit of what can be achieved, slight modifications are enough to simulate the Turing machine. In [6] simulation of Turing machines was achieved in 3D and was done almost surely by introducing probabilities. It was also achieved by introducing negative glue weights [24], by considering polyomino tiles [10], polygonal tiles [13], detachable glues [15], or by performing the assembly in several steps [4]. Nevertheless, the question is still open for non-cooperative aTAM. Several recent studies hint that it is likely decidable: non-cooperative aTAM is not intrinsically universal [18, 22], it is not able to simulate the Turing machine in the classical way [22], and a 2D pumping lemma was published in [21]. A weaker version of non-cooperative aTAM called directed where only one final terminal assembly is allowed was shown to be decidable by combining [8] and [21].

Although all these results point towards a negative answer, if non-cooperative aTAM were undecidable, it would be a surprising breakthrough and could lead to surprising results. It is worth remembering that such a scenario had already occurred for Wang tiles: the domino problem was initially conjectured to be undecidable, and proving this conjecture wrong required exhibiting aperiodic tilings. In this context, aperiodicity is an unusual way of initializing computation. Subsequently, aperiodic tilings were extensively studied and became a model of crystallography.

Concerning the complexity of non-cooperative aTAM, assembling rectangles and squares in 3D was achieved in [11, 12], and the upper and lower bounds on the number of tile types almost match. In 2D, lower bounds are known for the case in which mismatches are disallowed [16]. Concerning the main 2D model, the existence of efficient paths of size nlogn was shown in [19] (improving on a previous construction in [17]). An efficient path appears in every terminal assembly and only requires a tile set of size n, whereas an auxiliary path may appear somewhere else in the terminal assembly. A limitation of this approach was also obtained in [21]: it is impossible to construct efficient paths of arbitrary lengths. Concerning the directed non-cooperative aTAM, the work [20] – an update of [8] – shows that only four kinds of terminal assemblies exist, one of them being a bi-periodic grid which must be hardcoded in the tile set.

1.2 Our contribution

In this paper, we consider another one of this four kinds of assemblies: the finite terminal assembly. Our main result is a linear bound (in the number of tile types) on the size of finite terminal assemblies. Besides advancing the understanding of directed non-cooperative aTAM, this result has several major implications. Firstly, it partially solves a conjecture stated in [27, 32] about the asymptotic bound on assembling a square which is now proven to be linear. Note that finding the exact multiplicative constant is still an open question. Secondly, it is another hint that directed non-cooperative aTAM is not able to perform any complex computation. Thirdly, our result highlights a fundamental difference with non-cooperative aTAM: concurrency is required to assemble the efficient paths exhibited in [19]. Fourthly, our bound opens new perspectives for improving several previous results such as the pumping lemma in [21]. Indeed, multiple major results rely on understanding the “information flow” in an assembly, like for example the window movie lemma stated in [18]. Intuitively, a window delimits an area of the plane and a window movie is the order of placement, position, and glue types appearing along the window. The main theorem in [21] was obtained by focusing on a particular window movie and two of its critical glues. In this paper, we improve on the previous reasoning by showing that some information flowing through the window cannot be new and is therefore redundant. A similar approach has also recently been used to show that some fractals cannot be assembled in the cooperative case [3]. Using such improved tools may have consequences for other model and results.

Due to space constraints, we present only here the key ideas arranged in a roadmap and explain how they articulate in the proof of the main result which is available on arXiv [14].

2 Abstract tile assembly model

As usual, let be the set of real numbers, let be the set of all integers, let be the set of all natural numbers including 0, and let be the set of all natural numbers excluding 0. The domain of a function f is denoted dom(f), and its range (or image) is denoted f(dom(f)).

2.1 General definitions and main theorem

A tile type is a unit square with four sides, each consisting of a glue type and a nonnegative integer strength. Let T be a finite set of tile types. The sides of a tile type are respectively called north, east, south, and west.

An assembly is a partial function α:2T where T is a set of tile types and the domain of α (denoted dom(α)) is connected.111Intuitively, an assembly is a positioning of unit-sized tiles, each from some set of tile types T, so that their centers are placed on (some of) the elements of the discrete plane 2 and such that those elements of 2 form a connected set of points. Two tile types in an assembly are said to bind (or interact, or to be stably attached) if the glue types on their abutting sides are equal, and have strength 1. An assembly α induces an undirected weighted binding graph Gα=(V,E), where V=dom(α), and there is an edge {a,b}E if and only if the tiles at positions a and b interact, and this edge is weighted by the glue strength of that interaction. The assembly is said to be τ-stable if every cut of Gα has weight at least τ.

Given two τ-stable assemblies α and β, the union of α and β, written αβ, is an assembly defined if and only if and for all pdom(α)dom(β), α(p)=β(p) and either at least one tile of α binds with a tile of β or dom(α)dom(β). Then, for all pdom(α), we have (αβ)(p)=α(p) and for all pdom(β), we have (αβ)(p)=β(p).

A tile assembly system is a triple 𝒯=(T,σ,τ), where T is a finite set of tile types, σ is a τ-stable assembly called the seed, and τ is the temperature. Throughout this article, τ=1.

Given two τ-stable assemblies α and β, we say that α is a subassembly of β, and write αβ, if dom(α)dom(β) and for all pdom(α), α(p)=β(p). We also write α1𝒯β if we can obtain β from α by the binding of a single tile type, that is: αβ, |dom(β)dom(α)|=1 and the tile type at the position dom(β)dom(α) binds to α at that position. We say that γ is producible from α if there is a (possibly empty) sequence α1,α2,,αn where n{}, α=α1 and αn=γ, such that α11𝒯α21𝒯1𝒯αn.

The set of productions, or producible assemblies, of a tile assembly system 𝒯=(T,σ,τ) is the set of all assemblies producible from the seed assembly σ and is written 𝒜[𝒯]. An assembly α is called terminal if there is no β such that α1𝒯β. The set of all terminal assemblies of 𝒯 is denoted 𝒜[𝒯]. If there is a unique terminal assembly, i.e. |𝒜[𝒯]|=1, then 𝒯 is directed and its unique terminal assembly is called γ along this paper.

The easternmost column of a finite assembly α is designated by eα=max{x:y,(x,y)dom{α}}, wα, nα, sα are defined similarly for the westernmost, northernmost and southernmost columns of the assembly respectively. The horizontal width of an assembly α is eαwα and its vertical height nαsα. The following theorem is the main contribution of this paper.

Theorem 1.

Consider a directed tile assembly system (T,σ,1), if its terminal assembly γ is finite then its horizontal width and vertical height are bounded by 7|σ|+58|T|+30.

For the rest of the article, we consider a directed tile assembly system 𝒯=(T,σ,1) and we suppose that its terminal assembly γ is finite. Also, we assume that the assembly grows the furthest away from the seed to the east, i.e.:

eαeσ=max{eαeσ,nαnσ,|wαwσ|,|sαsσ|}.

With this assumption it is sufficient to bound eαeσ by 3|σ|+29|T|+15 to prove the main theorem. The proof of this result is constructive: we design an algorithm which takes as input an assembly γ such that eγ>3|σ|+29|T|+15 and it will either:

  • output a certificate that the tile assembly system is not directed;

  • bind a new tile to the assembly, showing that γ is not terminal.

By iterating this algorithm on a large enough finite assembly, we are able to make it grow arbitrarily large. Note that, by using the pumping lemma of [21], an infinite periodic path can be built when the assembly is large enough. We do not explicitly write the algorithm in this paper, but it can be directly derived from the constructive proofs, which are concluded by exhibiting a contradiction: either γ is not terminal, or the tile assembly system is not directed.

3 State of the art, roadmap and main obstacles

Our proof starts by following the same steps as the ones done in [21]. In Subsections 3.1, 3.2, 3.3 and 3.4, we present the reasoning and the tools necessary to construct a specific assembly called the shield. Our proof then diverges from previous approaches, as shields were complex to assemble, despite being useful in proving the pumping lemma in [21]. Nevertheless, in Subsection 3.5, we show that shields take a simple form when the terminal assembly of a directed tile assembly system is finite. In Subsection 3.6, we explain the key idea on how to use shields in an original way to obtain the main result of this paper. Note that this article is only a roadmap: we identify several technical difficulties, called locks, which are solved in the extended version [14].

3.1 Paths

Since there is no possible synchronization between the tiles in the non-cooperative case, we focus on paths instead of assemblies. Formally, a path P is a finite sequence of tiles (Pi)0i|P|1 such that each tile Pi interacts with the next one Pi+1 of the sequence. Moreover, a path does not intersect with the seed and is simple: two different tiles of P do not occupy the same position. The length of P is the size |P|1 of the sequence. If the first tile of the path interacts with a tile of the seed σ then the path is producible. The last tile of a producible path is the easternmost one if and only if it is the only tile of P on column eP with eP>eσ; moreover, a producible path is extremal if eP=eγ (we remind that γ is the unique terminal assembly). We say that a path P is a subassembly of γ if and only if each tile of P belongs to γ. Of course, producible and extremal paths are subassemblies of γ.

We now introduce some basic operations on paths. The concatenation of a finite path P with a path Q is the concatenation PQ of these two paths as sequences. PQ is a path if and only if (1) the last tile of P interacts with the first tile of Q and (2) P and Q do not intersect. For a path P=P0PiPi+1Pj, we define the subpath of P between indices i and j, both included, in the following way: Pi,i+1,,j=PiPi+1Pj. In the special case of a subpath where i=0 (resp. j=|P|1), we say that P0,1,,j (resp. Pj,,|P|1) is a prefix (resp. suffix) of P. Consider a vector v2 and a tile A, the translation of A by v is the tile A+v=(pos(A)+v,type(A)). The translation of a path P by v is P+v=(P0+v)(P1+v)(P|P|1+v). Consider two indices 0ij|P|1, by abuse of notation we designate by PiPj the vector pos(Pi)pos(Pj). Also, we denote by glue(PiPj) the glue used to bind tile Pi with Pi+1. It is situated on a glue column c between the two tiles (and thus between two columns c0.5<c<c+0.5). The assembly asm(P) is the representation of the path P as an assembly (the order of the tiles is not taken into account anymore). This notation allows to merge two paths P and Q as asm(P)asm(Q). This operation can be done even if P and Q intersect and thus is more general than the concatenation.

Figure 1: An extremal path P and the different bounds used during the analysis. Along the different figures, the seed is always shown in black tiles. This path P crosses column 5, leading to the contradiction implying that the terminal assembly is in fact infinite.

The previous results of [21] and the ones of this paper are obtained by showing that the farther away a path grows from the seed, the more it is constrained. Figure 1 shows an extremal path and several bounds. The main one 5 is the bound used to prove the main Theorem 1: if a path crosses this column then the terminal assembly is infinite. The bound 0 shows that an extremal path cannot grow too far to the west of the seed, i.e. on the opposite side of the seed from its last tile.

Lock 1.

If P is an extremal path, then wP0=wσ2|T|1.

This result was also proven in [36], in a slightly different context. A simplified proof of this result in [14].

The path P will be cut in three parts. The first one is its beginning (in pale green in Figure 1) which is too close to the seed to be useful222That is because the visible glues between the columns B0 and B1 will point east. The notion of a visible glue is formally introduced in the next subsection.. The middle of the path P (in green in Figure 1) will start on a column with index at least 1=eσ+|T|+1.5 and will end on a column with index at most 2=eσ+5|T|+1.5 (the exact beginning and ending of this subpath of P are explained in Figure 2 and Subsection 3.4). In this subpath of P, we aim to locate two indices 0ij|P|1 such that glue(PiPi+1) and glue(PjPj+1) have the same type, allowing us to try to assemble P0,,i(Pj+1,,|P|1+PjPi) or P0,,j(Pi+1,,|P|1+PiPj). Note that copying and pasting the end of P is not always possible due to possible intersections between the beginning of P and its translated suffix. Thus, one key step explained in Subsections 3.4 and 3.5 is to select i and j such that P0,,i(Pj+1,,|P|1+PjPi) is always a producible path. Finally, the end of the path P (in dark green in Figure 1) has to be large enough such that when it is copied and pasted, it will create a large obstacle, called a shield. This shield will be used to find other indices where different parts of P can be copied and pasted. Repeating this reasoning will eventually lead to a contradiction. The role of bounds 3 and 4 will be explained in Subsection 3.6, we do not give here their explicit definition since their values depend on the positions of Pi and Pj.

3.2 Visible glues of an extremal path

All results of this paper rely on the notion of visible glues introduced in [22]. Consider an index 0i|P|1, glue(PiPi+1) is horizontal if both tiles are on the same line or vertical if both tiles are on the same column. A horizontal glue points east if Pi is west of Pi+1 otherwise it points west. The glue is visible from the south (resp. north) in P if and only it is the southernmost (northernmost) glue of P on its column and if there are no tiles of the seed on both adjacent columns. We designate by li the glue ray associated to glue(PiPi+1): li is a ray starting at the position of glue(PiPi+1) going south (resp. north) if glue(PiPi+1) is visible from the south (resp. north). If the last tile of a producible path P is the easternmost one (which is the case for an extremal path) then we have the following properties (see Figure 2):

Figure 2: The path P of Figure 1 with some visible glues: all glues visible from the north are pointing east (by Lemma 1) and glue(Pi1Pi1+1) is an example of a glue visible from the south and pointing west. The glue(Pi3Pi3+1) is the westernmost glue visible from the south and pointing east. This glue is on a glue column c=11 in this example (by Lock 2, c1). The last glue of P, glue(Pi7Pi7+1), is always visible from the south and from the north. The glue(Pi4Pi4+1) and the glue(Pi5Pi5+1) are visible from the south and north respectively and form an upward span, see Figure 3. The limit between the pale green and green subpaths is delimited by glue(Pi2Pi2+1) which is the first glue of the span of P on glue column 1. The limit between the green and dark green subpaths is delimited by the last glue of P on glue column 2 which happens to be glue(Pi6Pi6+1) in this simple example.
Fact 1.

Consider a producible path P whose last tile is the easternmost one. Then up to some symmetries333Swapping the north and south glues of all tile types leads to horizontal symmetry of the producible assemblies., we can consider that all the glues of P which are visible from the north point east.

Lemma 2.

Consider a producible path P whose last glue is visible from the north. Then there exists a glue column c such that all glues visible from the south on glue column c<c point west and all glues visible from the south on glue column cc point east.

Lock 2.

Consider a producible path P whose last tile is the easternmost one and 0i|P|1 such that glue(PiPi+1) is visible from the south on glue column 1. Then glue(PiPi+1) points east.

Lemma 3.

Consider a producible path P whose last glue is visible from the north and indices 0i<j<|P|1 such that glue(PiPi+1) and glue(PjPj+1) are both visible from the south on glue columns c and c respectively. If both glues points east (resp. west) then c<c (resp c>c).

If P is an extremal path, then these three lemmas and Lock 2 imply that all glues which are visible from the north or south in P on a glue column c1 point east. The proofs of these lemmas are, now, classic results available in [21, 22] and will not be proven here again. The proof of Lock 2 is available in [21] and relies on a complex intermediate lemma whose proof is simplified in [14].

3.3 Cut, span and workspace

Combining two visible glues of a producible path P allows us to delimit a part of 2 which is an entire vertical half-plane, plus some other parts depending on the exact shape of P between the two visibles glues. When the visible glues are chosen appropriately, this area does not contain any tile of σ or any tile of P before the first visible glue. Then, we are free to edit P in this area without fearing a conflict with one of its previous parts or the seed. More formally, consider two indices 0s|P|2 and 0n|P|2 such that glue(PsPs+1) and glue(PnPn+1) are visible from the south and from the north respectively in P. If sn (resp. ns), (s,n) (resp. (n,s)) is called an upward (resp. downward) cut of P because the bi-infinite curve made of ls, Ps,,n+1 and ln cuts the space in two areas, see Figure 3. If glue(PsPs+1) (resp. glue(PnPn+1)) points east then the seed and the beginning of P are in the west side of the cut and cannot block the growth of new paths in the east side of the cut. The east side of the cut is called the workspace of the cut (s,n) (resp. (n,s)) of P, denoted by 𝒞:

Fact 2.

Consider a producible path P, a cut (s,n) of P and a path Q such that Q0 interacts with Ps and Q is in the workspace 𝒞 of the cut (s,n) of P444Note that tiles are placed on the discrete plane 2 but a workspace is a part of 2. For a path Q, this implies that Q is in 𝒞 if and only if the tiles of Q are in the area but also the segments linking the different tiles (including the glues).. Then P0,,sQ is producible.

(a)

(b)

Figure 3: (a) The upward span (s,n) of path P from Figure 2, with s=i4 and n=i5. The subpath P0,,s is shown in green, and Ps+1,,n in yellow. This span points east. The workspace 𝒞 of this span is drawn in blue and is delimited by ls (the glue ray of glue(PsPs+1)), Ps,,n+1 and ln (the glue ray of glue(PnPn+1)). (b) A path Q (in magenta) which is in 𝒞 and such that Q0 interacts with Ps. According to Fact 2, P0,,sQ is producible.

Along the paper, we will often consider the special case where the two visible glues s and n are on the same glue column. In this case, the cut is called the span of P on glue column c. The type of a span is the type of glue(PsPs+1) (resp. glue(PnPn+1)), it points in the same direction as glue(PsPs+1) (resp. glue(PnPn+1)), and its width is yPnyPs.

3.4 Classical reasoning, right-priority and shield

The result of [21] is obtained by combining two spans of the same type and direction. Indeed, consider an extremal path P and two glue columns 1c<c2 such that the spans (s,n) and (s,n) of P on glue columns c and c respectively have the same characteristics (they are both upward or downward spans, point east and have the same type). Then we can try to assemble P0,,s(Ps+1,,|P|1PsPs) or P0,,s(Ps+1,,|P|1+PsPs). To explain what may occur when trying to assemble such paths, we use the extremal path P of Figure 4(a) as an example.

(a)

(b)

(c)

(d)

Figure 4: (a) The upward spans (s,n) and (s,n) of a path P. The workspace 𝒟 of span (s,n) is in yellow. The beginning P0,,s of the path is in green, the middle Ps+1,,s of the path is in yellow and the end Ps+1,,|P|1 of the path is in blue. (b) We try to assemble Q=Ps,,|P|1+PiPj at the end of P0,,s for as long as possible. The tiles of Q are in orange and magenta, the orange ones are common to Q and P. (c) Since the tile assembly system is directed, Q can merge with P. (d) We try to assemble Ps+1,,|P|1PiPj at the end of P0,,s for as long as possible. The workspace 𝒞 of the span (s,n) is in blue.

In Figure 4(a), the spans (s,n) and (s,n) are upward spans and 𝒟 is the workspace of (s,n). In Figure 4(b), we try to assemble the path Q=Ps+1,,|P|1+PsPs at the end of P0,,s. While doing so, the following important events occur in this example. Firstly, there exists an index 0i|Q|1 such that Q0,,i grows along Ps+1,,|P|1 by putting its tiles in the same positions, i.e. for all 0ti, we have pos(Qt)=pos(Ps+1+t) (the tiles in orange in Figure 4(b)). Secondly, Q turns right of Ps,,|P|1 at pos(Qi) (for a formal definition of this notion see [21, 22]) and stays inside 𝒟 until it intersects with P at pos(Pk)=pos(Qj). Thirdly, Q leaves 𝒟 after Qj, i.e. no tiles of Qj+1,,|Q|1 are inside 𝒟. Fourthly, Q intersects with P0,,s. Thus P0,,sQ is not self-avoiding and is not a path but P0,,sQ0,,j is a path and it is producible by Fact 2. Moreover, since the tile assembly system is directed then we have Pk=Qj and Q0,,i=Ps+1,,s+1+i is the largest common prefix of Q and Ps+1,,|P|1.

Now, we focus on the fact that Q turns right of Ps+1,,|P|1. This event implies that Ps+1,,|P|1PsPs turns left of Ps,,|P|1, see Figure 4(d). By doing so, Ps+1,,|P|1PsPs immediately leaves the workspace 𝒞 of the span (s,n) of P. In this example, Ps+1,,|P|1PsPs quickly collides with P0,,s. Then, in the general case we have three possibilities:

Fact 3.

Consider an extremal path P and two glue columns 1c<c2 such that the spans (s,n) and (s,n) of P on glue columns c and c respectively have the same characteristics. Then one of the following holds:

  1. 1.

    Ps(Ps+1,,|P|1PsPs) turns right of Ps,,n+1;

  2. 2.

    or Ps(Ps+1,,|P|1+PsPs) turns right of Ps,,|P|1;

  3. 3.

    or the width of span (s,n) is less or equal to the width of span (s,n).

When the first case of Fact 3 occurs, a suffix of (Ps+1,,|P|1PsPs) will be used as a shield. For the third case of Fact 3, it was proven in [21] that in this case the path P is pumpable or fragile which means that either the tile assembly system is not directed or that the terminal assembly is infinite. These events cannot occur in our setting. We do not explain this argument in the roadmap.

In Subsection 3.5, we will consider a specific setting where the second case of Fact 3 also leads to a contradiction. To do so, consider the tile Pk=Qj of Figure 4: it is the only intersection between Qi+1,,|Q|1 and Ps+1+i,,|P|1 in this simple example. Since the tile assembly system is directed, it is possible to “merge” these two paths together. Indeed, R=P0,,sQ0,,jPk+1,,|P|1 is a producible extremal path, see Figure 4(c). In [21], this operation is repeated several times to build a path called a shield. From this point on, our reasoning differs from [21] and we introduce a setting where shields take a very simple form. Indeed, P and R are both extremal paths. Moreover, they share the common prefix P0,,s+1+i. Nevertheless the path R turns right of P at tile Pi. Then, we say that R is more right-priority than P. This notion of right-priority implies an order on extremal paths. Moreover, since we consider a finite terminal assembly, there is a finite number of extremal paths. Thus, it is possible to choose a rightmost-priority one. For such a path, it is not possible to be in a case like in Figure 4(c) where there is an intersection between Ps+i+1,,|P|1 and Qi+1,,|Q|1.

3.5 Shield in the directed case with a finite terminal assembly

Our aim is to work in a setting where only the first case of Fact 3 is possible. To achieve this goal, we consider an extremal path P, two glue columns 1c<c2, and we let (s,n) be the span of P on glue column c and (s,n) the span of P on glue column c, for an example see Figure 5.

Figure 5: The path P of Figure 1. We consider two upward spans (s,n) and (s,n) of P on columns 1c<c2 respectively. Both spans point east and we suppose that glue(PsPs+1)=glue(PsPs+1).

To eliminate the second case of Fact 3 where Ps(Ps+1,,|P|1+PsPs) turns right of Ps,,|P|1, we consider that P is not an arbitrary chosen path but that P is chosen wisely to have the following property.

Definition 4.

Consider an extremal path P, a glue column 1c2 and the span (s,n) of P on glue column c. If (s,n) is an upward (resp. downward) span then consider the set of extremal paths 𝒫 such that a path Q belongs to 𝒫 if and only if P0,,s+1 is a prefix of Q and glue(QsQs+1) is visible from the south (resp. north) in Q. Then P is a good path for glue column c if and only if it is the rightmost (resp. leftmost) priority path of 𝒫.

Figure 6: Only the end Ps,,|P|1 of the path P of Figure 5 is drawn. The workspace 𝒟 of the span (s,n) is in yellow. This workspace is cut in two areas 𝒟 and 𝒟+ by using the ray starting in pos(P|P|1) and going south. A path Q starting at tile Ps+1 is shown in orange and magenta. This path turns right of Ps,,|P|1 and it cannot leave 𝒟+ without intersecting the column eP+1, ls or Ps+1,,|P|1. The tiles in orange are shared between Q and Ps+1,,|P|1.

In the extended version of the paper [14], we will use a slightly weaker version of this property and we will consider canonical paths instead of good paths. Nevertheless, we do not enter into this level of details here. The following lemma explains how to find a good path.

Lemma 5.

Consider a glue column 1c2, there exists a good path P for glue column c.

Proof.

Consider 1c2, the set 𝒬 of extremal paths and let

w=min{width of the span of Q on glue column c:Q𝒬}.

We consider Q𝒬 such that the span (s,n) of Q on glue column c is of width w (note that several paths of 𝒬 may be of width w, any of them can be chosen as Q. Depending of this choice different good paths for column c can be found) and suppose that this span is an upward (resp. downward) span. Let P be the rightmost (resp. leftmost) priority extremal path such Q0,,s+1 is a prefix of P and glue(PsPs+1) is visible from the south (resp. north) in P. We claim that P is a good path for glue column c.

(a)

(b)

Figure 7: (a) A path Q and its upward span (s,n) on column c. To transform this path into a good one for column c, we consider the rightmost priority path P (represented in Figure 7(b)) which admits Q0,,s+1 as a prefix and which does not cross ls. (b) In this case, the span (n,s) of P on column c is a downward span (n,s) with n<s. Nevertheless, the width of this span is strictly less than the width of Q on column c, contradicting the definition of Q.

By definition and since glue(PsPs+1)=glue(QsQs+1), glue(PsPs+1) is visible from the south (resp. north) in P on glue column c. Let n such that glue(PnPn+1) is visible from the north (resp. south) on glue column c.

  • If sn then (s,n) is the upward (resp. downward) span of P on glue column c and P is a good path for glue column c.

  • Otherwise, s>n then (n,s) is a downward (resp. upward) span of P on glue column c, see Figure 7. In this case P is not a good path for glue column c. Nevertheless, since s>n then Pn=Qn (since Q0,,s is a prefix of P by definition of P). Moreover, since glue(QnQn+1) if visible from the north (resp. south) in Q then yPn<yQn (resp. yPn>yQn). This means that the width of the span of P on glue column c is strictly less than the width w of the span of Q on glue column c which contradicts the definition of w.

Thus, only the first case can occur and P is a good path.

Lock 3.

When the span (s,n) of a path P on glue column 1c2 is considered, the path P must be a good/canonical path for glue column c.

For the moment, assume that the extremal path P is a good path for glue column c. If the second case of Fact 3 occurs, Ps(Ps+1,,|P|1+PsPs) turns right of Ps,,|P|1 and a contradiction can be found. Indeed, let Q=Ps+1,,|P|1+PsPs and suppose that P0,,sQ is a producible path. Since c<c then xPs<xPs and eQ>eP=eγ. This is a contradiction with the fact that P is extremal, since P0,,sQ goes further east than P by cc columns. Then by Fact 2, Q must leave the workspace 𝒟 of the span (s,n) of P but if Q turns right of Ps,,|P|1, all cases lead to contradictions (see Figure 6):

  • if Q crosses ls: then QPsPs=Ps+1,,|P|1 intersects lsPsPs=ls contradicting the fact that glue(PsPs+1) is visible from the south;

  • if Q intersects Ps+1,,|P|1: then either P intersects itself or P is not a good path for glue column c because a more right-priority path exists (by a reasoning similar to the one of Figure 4(c));

  • if Q crosses ln: then to reach this ray requires either to cross Ps+1,,|P|1 which is the previous case or to put a tile on column x|P|1+1=eγ+1 which contradicts that P is extremal.

Then the second case of Fact 3 cannot occur if P is a good path for column c, meaning that only the first case is possible, in which Ps,,|P|1PsPs must turn right of Ps,,n+1. Similarly, assume that P is also a good path for glue column c and consider the workspace 𝒞 of the span (s,n) of P (see Figure 8). This workspace can be cut in two areas 𝒞+ and 𝒞 by the ray starting at pos(P|P|1) and going south. The path Ps+1,,|P|1PsPs can be written as CS where C is the largest common prefix between Ps+1,,|P|1PsPs and Ps+1,,n, and S is the rest of the path Ps+1,,|P|1PsPs. The path S is a called a shield of span (s,n) and by a similar reasoning S is inside the workspace 𝒞+ and does not insect with P. Indeed, the path S cannot intersect with P (since P is simple and a good path for glue column c), cannot reach column xP|P|1+1 (since P is extremal) or cross ls (since Ps,,|P|1 cannot intersect ls). Note that the exact definition of a shield is more involved and is given in [14]. Nevertheless, the definition of S as a shield is correct in the context of good paths.

Figure 8: We consider the path P of the Figure 3, the workspace 𝒞 of its span (s,n) is in blue and is cut in two areas 𝒞+ and 𝒞 by the ray starting at pos(P|P|1) and going south. The path Ps+1,,|P|1PsPs can be written as CS: the tiles of C are in common between Ps+1,,|P|1 and Ps+1,,|P|1PsPs and they are drawn in orange while the tiles of S are drawn in cyan. The path S is called a shield, it does not intersect P and it is in 𝒞+.

3.6 Pseudo-visibility

We consider the span (s,n) of a path P on a glue column 1c2. In this subsection, we explain how a shield S of this span can be used to find a protected and pseudo-visible glue on glue column c, and we list the assumptions done to obtain this result. Such a glue will have properties similar to those of a visible glue. Then, when Fact 3 is used on two spans with the same characteristics, either a shield or a contradiction is obtained. If a shield is obtained then a new protected and pseudo-visible glue can be found. This glue behaves as a visible glue and will replace the one consumed by using Fact 3. We start by defining a pseudo-visible glue, see Figure 9.

Definition 6.

Consider an extremal path P, a glue column 1c2 and an index 0d|P|1. We say that glue(PdPd+1) is pseudo-visible from the south (resp. north) if and only if glue(PdPd+1) is the southernmost (resp. northernmost) glue of Pd,,|P|1 on glue column c and points east.

Figure 9: We consider the path P of the Figure 8 and its shield S (in cyan). Here, glue(PdPd+1) is the southernmost glue of Pd,,|P|1 on glue column c, and it is pseudo-visible from the south in P. Remark that glue(SiSi+1) is on column c and the path P does not intersect the segment between glue(SiSi+1) and glue(PdPd+1). In this case, the shield S protects glue(PdPd+1).

Consider sdu|P|1 such that glue(PdPd+1) is pseudo-visible from the south (resp. north) on glue column c and glue(PuPu+1) is visible from the north (resp. south) in Pd,,|P|+1 on glue column c then (u,d) is an upward (resp. downward) pseudo-span. Consider, the workspace 𝒞 associated to the cut (d,u) of Pd,,|P|1. The pseudo-span (d,u) is visible if and only if, for any path Q such that Q is in 𝒞 and Q0 interacts with Pd, P0,,dQ is producible. Note that any span is a visible pseudo-span but a pseudo-span is not necessarily visible, see Figures 10 and 11. Intuitively, a visible pseudo-span behaves like a span. Shields will be used to find new visible pseudo-spans (in particular those which are not spans).

Figure 10: Following Figure 9, we represent here the pseudo-span (d,n) of the path P with its workspace 𝒞 in cyan. The beginning of the path P is not shown. Consider a path Q such that Q0 binds with Pd and Q is in 𝒞. The orange tiles are common between Q and Pd,,n while the red tiles belong only to Q.
Figure 11: Following Figure 10, we try to assemble P0,,dQ but the last tile of Q conflits with P0,,d. Hence, the pseudo-span (d,n) is not visible. In this figure, only the beginning P0,,d is shown.

The proof of the main Theorem 1 is done by showing that the larger the path is, the more constrained it is. The first proven bound, in [21], uses only two glues per glue column: the glue visible from the north and the glue visible from the south. When the proof requires more glues to find a contradiction, a new glue column is considered. Here, shields will be used to locate visible pseudo-span, allowing to work with more than two glues per glue column. Now, we explain how to locate a visible pseudo-span on a simple case where several hypotheses on the shield are assumed. These hypotheses will allow a shield to protect a glue of P. The general case is far more complex and is solved in [14].

Let S be a shield of the span (s,n) of P and consider s<d|P|1 of P such that glue(PdPd+1) is on glue column c and pointing east. If there exists 0i|S|1 such that glue(SiSi+1) is on glue column c and no glue of P is on glue column c between glue(PdPd+1) and glue(SiSi+1), then glue(PdPd+1) is protected by shield S, see Figure 9. Note that, we propose here a simplified definition of a protected glue which is sufficient for the roadmap. The formal definition is given in [14]. First, remark that shield S must intersect glue column c to be useful according to this definition.

Lock 4.

Consider an extremal path P such that P is a good path on glue column 1c2. Let S be a shield of the span (s,n) of P on glue column c. Then, a glue of S is on glue column c.

How to find a protected glue when a shield satisfies the hypothesis of Lock 4 is explained in [14]. In this roadmap, we assume that this protected glue is pseudo-visible.

Lock 5.

Consider an extremal path P and a span (s,n) like in Lock 4. There exists sd|P|1 such that glue(PdPd+1) is pseudo-visible and protected by shield S.

Moreover, we also add this condition to avoid complex cases which are discussed later.

Lock 6.

Consider an extremal path P, a span (s,n) as in Lock 4 and an index sd|P|1 as in Lock 5. Then dn.

It follows from Locks 5 and 6 that (d,n) is a pseudo-span. According to Lock 4, shield S protects glue(PdPd+1). These hypotheses are sufficient to show that the pseudo-span (s,n) is visible.

Lock 7.

Consider an extremal path P with a span (s,n) like in Lock 4, and an index sd|P|1 satisfying the property in Lock 6. Then the pseudo-span (d,n) of P is visible.

To obtain this result, consider a path Q such that Q0 interacts with Pd and Q is inside the workspace 𝒞 of the pseudo-span (d,n) of P as shown in Figures 10 and 11. In this example, P0,,dQ is not a path since the last tile of Q intersects with P0,,d. Note furthermore that Q also intersects shield S (Figure 12). Then, by merging parts of P, Q, and S, we obtain a more right-priority path as shown in Figure 13, which contradicts the assumption that P is a good path for glue column c.

Another way for Q to collide with P0,,d is to avoid S by turning around it. To do so, Q must grow to the east and then go back to the west, see Figure 13. This pattern is called a U-turn and a key point of the proof of the pumping lemma [21] is to prove that there is a contradiction if the U-turn is long enough. A quadratic bound was proven in [21]. To obtain the main result of this work, we must improve this bound to a linear one. Solving Lock 7 is done in two steps, see Figure 13 for an illustration.

Figure 12: We merge parts of paths P and Q, and of shield S from Figures 9, 10, and 11, to obtain a new path which is more right-priority than P, contradicting that P is a good path for glue column c. Such merging is possible since the tile assembly system is directed. The tile common to Q and S is shown in orange.
Figure 13: Since the case shown in Figure 12 leads to a contradiction, we consider another case. Here, the path Q tries to collide with P0,,d by avoiding the shield S by turning around it. To do so, Q must first reach glue column 4 and come back to glue column 3.
Lock 8.

eP0,,d is bounded by 3=2cwσ+3|T|+2 (we remind that σ is the seed and the span (s,n) of P is on glue column c).

Lock 9.

Consider a path Q inside the workspace 𝒞 of the pseudo-span (d,n) of P, such that Q0 interacts with Pd. If there exists 0i|Q|1 such that glue(QiQi+1) is on glue column 4=c+3|σ|+24|T|+14 (we remind that σ is the seed and the span (s,n) of P is on glue column c), then there is no index i<j|Q|1 such that glue(QjQj+1) is visible in Q on glue column 3.

Informally, these two locks capture the intuition that shield S is an obstacle preventing any collision between Q and P0,,d, and ensures that pseudo-span (d,n) is visible.

If all these arguments hold then we can consider 2|T|+1 spans of P which are located on different glue columns between 1=eσ+|T|+1.5 and 2=eσ+5|T|+1.5. By the pigeonhole principle, two of these spans have the same direction and type. According to the reasoning presented so far, either there is a contradiction (P is not extremal or P is not a good path for a given column) or a shield can be assembled which can be used to find a visible pseudo-span. In the considered collection of 2|T|+1 spans, one of them can be replaced by this new visible pseudo-span. Note that the new pseudo-span is narrower than the replaced one. By iterating this reasoning, we eventually find a contradiction.

3.7 Summary of the main obstacles

In Section 4 of the extended version [14], we start by explaining how to build a canonical path for a glue column 1c2, solving Lock 3. A canonical path is obtained by slightly modifying a good path. These modifications are done to deal with Lock 6. In Section 5 of [14], we give a linear bound on the length of U-turns, solving Locks 8 and 9 (and thus Lock 7). Alongside the tools developed in this section, we remind the arguments of [36] to solve Lock 1 and the arguments of [21] to solve Lock 2. Thirdly, we introduce in Section 6 of [14] the decomposition of a canonical path P on glue column c into arcs555This decomposition was first introduced in [36] but was later abandoned in the final version of the paper after some simplifications. to solve Lock 5. This decomposition allows to find protected glues which are not pseudo-visible. In Section 7 of [14], we give the formal definition of a shield and put all arguments together to prove the main Theorem 1 by following the reasoning of this roadmap. The proof of the extended version [14] ends with the special case of Lock 4.

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