ℓ-CTP: Utilizing Multiple Agents to Find Efficient Routes in Disrupted Networks

Recent hurricane seasons have demonstrated the need for more effective methods of coping with flooding of roadways. A key complaint of logistics managers is the lack of knowledge when developing routes for vehicles attempting to navigate through areas which may be flooded. In particular, it can be difficult to re-route large vehicles upon encountering a flooded roadway. We utilize the Canadian Traveller’s Problem (CTP) to construct an online framework for utilizing multiple vehicles to discover low-cost paths through networks with failed edges unknown to one or more agents a priori. This thesis demonstrates the following results: first, we develop the ℓ-CTP framework to extend a theoretically validated set of path planning policies for a single agent in combination with the iterative penalty method, which incentivizes a group of ℓ \u3e 1 agents to explore dissimilar paths on a graph between a common origin and destination. Second, we carry out simulations on random graphs to determine the impact of the addition of agents on the path cost found. Through statistical analysis of graphs of multiple sizes, we validate our technique against prior work and demonstrate that path cost can be modeled as an exponential decay function on the number of agents. Finally, we demonstrate that our approach can scale to large graphs, and the results found on random graphs hold for a simulation of the Houston metro area during hurricane Harvey

The Need for Seed (in the abstract Tile Assembly Model)

In the abstract Tile Assembly Model (aTAM) square tiles self-assemble, autonomously binding via glues on their edges, to form structures. Algorithmic aTAM systems can be designed in which the patterns of tile attachments are forced to follow the execution of targeted algorithms. Such systems have been proven to be computationally universal as well as intrinsically universal (IU), a notion borrowed and adapted from cellular automata showing that a single tile set exists which is capable of simulating all aTAM systems (FOCS 2012). The input to an algorithmic aTAM system can be provided in a variety of ways, with a common method being via the "seed" assembly, which is a pre-formed assembly from which all growth propagates. In this paper we present a series of results which investigate the the trade-offs of using seeds consisting of a single tile, versus those containing multiple tiles. We show that arbitrary systems with multi-tile seeds cannot be converted to functionally equivalent systems with single-tile seeds without using a scale factor > 1. We prove tight bounds on the scale factor required, and also present a construction which uses a large scale factor but an optimal number of unique tile types. That construction is then used to develop a construction that performs simultaneous simulation of all aTAM systems in parallel, as well as to display a connection to other tile-based self-assembly models via the notion of intrinsic universality.Comment: To appear in the SODA 2023 proceeding

Self-Replication via Tile Self-Assembly (Extended Abstract)

In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues. These modifications consist of an extension to 3D, the ability of tiles to form "flexible" bonds that allow bound tiles to rotate relative to each other, and allowing tiles of multiple shapes within the same system. We call this new model the STAM*, and we present a series of constructions within it that are capable of self-replicating behavior. Namely, the input seed assemblies to our STAM* systems can encode either "genomes" specifying the instructions for building a target shape, or can be copies of the target shape with instructions built in. A universal tile set exists for any target shape (at scale factor 2), and from a genome assembly creates infinite copies of the genome as well as the target shape. An input target structure, on the other hand, can be "deconstructed" by the universal tile set to form a genome encoding it, which will then replicate and also initiate the growth of copies of assemblies of the target shape. Since the lengths of the genomes for these constructions are proportional to the number of points in the target shape, we also present a replicator which utilizes hierarchical self-assembly to greatly reduce the size of the genomes required. The main goals of this work are to examine minimal requirements of self-assembling systems capable of self-replicating behavior, with the aim of better understanding self-replication in nature as well as understanding the complexity of mimicking it

Crystal structure and mutational analysis of human uracil-DNA glycosylase: Structural basis for specificity and catalysis

AbstractCrystal structures of the DNA repair enzyme human uracil-DNA glycosylase (UDG), combined with mutational analysis, reveal the structural basis for the specificity of the enzyme. Within the classic α/β fold of UDG, sequence-conserved residues form a positively charged, active-site groove the width of duplex DNA, at the C-terminal edge of the central four-stranded parallel β sheet. In the UDG-6-aminouracil complex, uracil binds at the base of the groove within a rigid preformed pocket that confers selectivity for uracil over other bases by shape complementarity and by main chain and Asn-204 side chain hydrogen bonds. Main chain nitrogen atoms are positioned to stabilize the oxyanion intermediate generated by His-268 acting via nucleophilic attack or general base mechanisms. Specific binding of uracil flipped out from a DNA duplex provides a structural mechanism for damaged base recognition

ℓ-CTP: Utilizing Multiple Agents to Find Efficient Routes in Disrupted Networks

Recent hurricane seasons have demonstrated the need for more effective methods of coping with flooding of roadways. A key complaint of logistics managers is the lack of knowledge when developing routes for vehicles attempting to navigate through areas which may be flooded. In particular, it can be difficult to re-route large vehicles upon encountering a flooded roadway. We utilize the Canadian Traveller’s Problem (CTP) to construct an online framework for utilizing multiple vehicles to discover low-cost paths through networks with failed edges unknown to one or more agents a priori. This thesis demonstrates the following results: first, we develop the ℓ-CTP framework to extend a theoretically validated set of path planning policies for a single agent in combination with the iterative penalty method, which incentivizes a group of ℓ > 1 agents to explore dissimilar paths on a graph between a common origin and destination. Second, we carry out simulations on random graphs to determine the impact of the addition of agents on the path cost found. Through statistical analysis of graphs of multiple sizes, we validate our technique against prior work and demonstrate that path cost can be modeled as an exponential decay function on the number of agents. Finally, we demonstrate that our approach can scale to large graphs, and the results found on random graphs hold for a simulation of the Houston metro area during hurricane Harvey

Universal Shape Replication via Self-Assembly with Signal-Passing Tiles (Extended Abstract)

In this paper, we investigate shape-assembling power of a tile-based model of self-assembly called the Signal-Passing Tile Assembly Model (STAM). In this model, the glues that bind tiles together can be turned on and off by the binding actions of other glues via "signals". In fact, we prove our positive results in a version of the model in which it is slightly more difficult to work (where tiles are allowed to rotate) but show that they also hold in the standard STAM. Specifically, the problem we investigate is "shape replication" wherein, given a set of input assemblies of arbitrary shape, a system must construct an arbitrary number of assemblies with the same shapes and, with the exception of size-bounded junk assemblies that result from the process, no others. We provide the first fully universal shape replication result, namely a single tile set capable of performing shape replication on arbitrary sets of any 3-dimensional shapes without requiring any scaling or pre-encoded information in the input assemblies. Our result requires the input assemblies to be composed of signal-passing tiles whose glues can be deactivated to allow deconstruction of those assemblies, which we also prove is necessary by showing that there are shapes whose geometry cannot be replicated without deconstruction. Additionally, we modularize our construction to create systems capable of creating binary encodings of arbitrary shapes, and building arbitrary shapes from their encodings. Because the STAM is capable of universal computation, this then allows for arbitrary programs to be run within an STAM system, using the shape encodings as input, so that any computable transformation can be performed on the shapes

Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair

Endonuclease V (EndoV) initiates a major base repair pathway for nitrosative deamination resulting from endogenous processes and increased by oxidative stress from mitochondrial dysfunction or inflammatory responses. We solved the crystal structures of Thermotoga maritima EndoV in complex with a hypoxanthine lesion substrate and with product DNA. The PYIP wedge motif acts as a minor-groove damage sensor for helical distortions and base mismatches and separates DNA strands at the lesion. EndoV incises DNA with an unusual offset nick one nucleotide 3′ of the lesion, as the deaminated adenine is rotated ~90° into a recognition pocket ~8Å from the catalytic site. Tight binding by the lesion recognition pocket in addition to Mg(2+) ion and hydrogen-bond interactions to the DNA ends stabilize the product complex, suggesting orderly recruitment of downstream proteins in this base repair pathway