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math.CO updates on arXiv.org

Complement Submodular Information Measures for Balanced and Robust Data Selection A Proof of a Conjecture on Positive and Negative Square Energies of Unicyclic Graphs Laplacian Spectrum of the Weakly Zero-Divisor Graph of a Finite Commutative Ring An identity for second Eulerian numbers via lattice-point counting $t$-tone edge coloring of graphs Constructing Maximal Bumpless Pipedreams for Double Grothendieck Polynomials Mubayi's Polynomial-Ideal Conjecture and Cover-Ideal Turán Methods Implicit Binarization via Complex Phase Dynamics in Combinatorial Optimization The limits of Schur multipliers in Pólya conversion problems for the $q$-permanent function Universality theorems for generalized splines Framing Triangulations for Arbitrary Integer Flow Polytopes On the Common Generalization of Gentle Algebras and Framed Directed Acyclic Graphs The complexity of frugal digraph homomorphisms Chaotic and periodic behavior of jeu de taquin on infinite Young tableaux Enumerating Pattern Avoiding Parking Functions Incidence toric ideals and three-point functions Unique Winning Opening Move in Three-Row Chomp Strong majority colorings of graphs A Balancing Theorem for Spanning Trees of Rectangular Grid Graphs Spectral radius and edge-disjoint connected factors of graphs New invariants for rank metric codes, with applications to the classification of rank two semifields of order 256 Flexible DP-4-coloring of planar graphs without 4-cycles and intersecting triangles Balanced intersection size distributions in projective planes List Reconstruction Problem with List Size Two Is Dimensionality a Barrier for Retrieval Models? The INIEP: Irreducible and Positive Realizations The number of Pfaffian orientations on punctured polygonally cellulated surfaces Explicit Construction of Polytopes whose Ehrhart Polynomials Realize any Given Sign Pattern Finite-state enumeration of adjacency-constrained 132-avoiding permutations AMDS and quantum AMDS Constacyclic codes of length $4p^ς$ over $\mathbb{F}_{{p}^{m}}$
The Role of Sequence Information in Minimal Models of Mol...
Jeremy Guntoro, Thomas Ouldridge · 2024-02-29 · via math.CO updates on arXiv.org

Sequence-directed assembly processes - such as protein folding - allow the assembly of a large number of structures with high accuracy from only a small handful of fundamental building blocks. We aim to explore how efficiently sequence information can be used to direct assembly by studying variants of the temperature-1 abstract tile assembly model (aTAM). We ask whether, for each variant, their exists a finite set of tile types that can deterministically assemble any shape producible by a given assembly model; we call such tile type sets "universal assembly kits". Our first model, which we call the "backboned aTAM", generates backbone-assisted assembly by forcing tiles to be added to lattice positions neighbouring the immediately preceding tile, using a predetermined sequence of tile types. We demonstrate the existence of universal assembly kit for the backboned aTAM, and show that the existence of this set is maintained even under stringent restrictions to the rules of assembly. We compare these results to a less constrained model that we call sequenced aTAM, which also uses a predetermined sequence of tiles, but does not constrain a tile to neighbour the immediately preceding tiles. We prove that this model has no universal assembly kit in the stringent case. The lack of such a kit is surprising, given that the number of tile sequences of length N scales faster than both the number and worst-case Kolmogorov complexity of producible shapes of size N for a sufficiently large - but finite - set of tiles. Our results demonstrate the importance of physical mechanisms, and specifically geometric constraints, in facilitating efficient use of the information in molecular programs for structure assembly.