Titlebook: DNA Computing and Molecular Programming; 24th International C David Doty,Hendrik Dietz Conference proceedings 2018 Springer Nature Switzerl

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++: Molecular Programming Language,allenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. This necessitates effective representation of computation using molecular components. While previous work established the Turing-completeness of chemical reactions, defining representat

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Morose

Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler,t of relatively few monomer types, but are constrained by errors in growth and the limited sequence space of orthogonal DNA sticky ends that program tile interactions. We present a tile set optimization technique that, through analysis of algorithmic growth equivalence, potentially sensitive error p

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A Content-Addressable DNA Database with Learned Sequence Encodings,ich media. Our strand designs address cross-talk in associative DNA databases, and we demonstrate a novel method for learning DNA sequence encodings from data, applying it to a dataset of tens of thousands of images. We test our design in the wetlab using one hundred target images and ten query imag

mitral-valve

Temporal DNA Barcodes: A Time-Based Approach for Single-Molecule Imaging,t binding of DNA strands to perform super-resolution fluorescence imaging. An interesting challenge in DNA nanoscience and related fields is the unique identification of single-molecules. While wavelength multiplexing (using fluorescent dyes of different colors) can be used to increase the number of

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,Hierarchical Growth Is Necessary and (Sometimes) Sufficient to Self-assemble Discrete Self-similar rowing assembly at each step, there are no tile assembly systems capable of self-assembling the discrete self-similar fractals known as the “H” and “U” fractals. We then show that in a related model which allows for hierarchical self-assembly, the 2-Handed Assembly Model (2HAM), there does exist a t

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Transcript Design Problem of Oritatami Systems,odel is a computation model of this phenomenon, which lets its sequence (transcript) of beads (abstract molecules) fold cotranscriptionally by the interactions between beads according to its ruleset. We study the problem of designing a transcript that folds into the given conformation using the give

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Freezing Simulates Non-freezing Tile Automata,s. In this work, we fuse a particular well-studied generalization of tile assembly (the 2. or .) with concepts from cellular automata such as states and state transitions characterized by neighboring states. This allows for a simplification of the concepts from active self-assembly, and gives us mac