Related papers: XTile: An Error-Correction Package for DNA Self-As…
Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization. At equilibrium, the structure is encoded through specific interactions,…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
Winfree (1998) showed that discrete Sierpinski triangles can self-assemble in the Tile Assembly Model. A striking molecular realization of this self-assembly, using DNA tiles a few nanometers long and verifying the results by atomic-force…
Designing components that can robustly self-assemble into structures with biological complexity is a grand challenge for material science. Proofreading and error correction is required to improve assembly yield beyond equilibrium limits,…
We present a strict separation between the class of "mismatch free" self-assembly systems and general aTAM systems. Mismatch free systems are those systems in which concurrently grown parts must always agree with each other. Tile…
Neural inductive program synthesis is a task generating instructions that can produce desired outputs from given inputs. In this paper, we focus on the generation of a chunk of assembly code that can be executed to match a state change…
Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
Assembling simulation software along with the associated tools and utilities is a challenging endeavor, particularly when the components are distributed across multiple source code versioning systems. It is problematic for researchers…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpora of malicious binaries, obtaining high-quality corpora of…
In this paper, we investigate the abilities of systems of self-assembling tiles which can each pass a constant number of signals to their immediate neighbors to create replicas of input shapes. Namely, we work within the Signal-passing Tile…
The Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
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…
The Pattern self-Assembly Tile set Synthesis (PATS) problem, which arises in the theory of structured DNA self-assembly, is to determine a set of coloured tiles that, starting from a bordering seed structure, self-assembles to a given…
Experiments have reached a monumental capacity for designing and synthesizing microscopic particles for self-assembly, making it possible to precisely control particle concentrations, shapes, and interactions. However, more physical insight…