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An object-oriented combinator chemistry was used to construct an artificial organism with a system architecture possessing characteristics necessary for organisms to evolve into more complex forms. This architecture supports modularity by…
Formal verification is increasingly recognized as a critical foundation for building reliable software systems. However, the need for specialized expertise to write precise specifications, navigate complex proof obligations, and learn…
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…
We present an algorithm to compute the primary decomposition of a submodule $\mathcal{N}$ of the free module $\Z[x_1, \ldots, x_n]^m$. For this purpose we use algorithms for primary decomposition of ideals in the polynomial ring over the…
Given a graph $G$ and collection of subgraphs $T$ (called tiles), we consider covering $G$ with copies of tiles in $T$ so that each vertex $v\in G$ is covered with a predetermined multiplicity. The multinomial tiling model is a natural…
We propose a general framework for solving inverse self-assembly problems, i.e. designing interactions between elementary units such that they assemble spontaneously into a predetermined structure. Our approach uses patchy particles as…
Cellular manufacturing (CM) is an approach that includes both flexibility of job shops and high production rate of flow lines. Although CM provides many benefits in reducing throughput times, setup times, work-in-process inventories but the…
Programs admitting a polyhedral representation can be transformed in many ways for locality and parallelism, notably loop tiling. Data flow analysis can then compute dependence relations between iterations and between tiles. When tiling is…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
In this paper, we introduce tiled graphs as models of learning and maturing processes. We show how tiled graphs can combine graphs of learning spaces or antimatroids (partial hypercubes) and maturity models (total orders) to yield models of…
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding…
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…
Tile-based self-assembly systems are capable of universal computation and algorithmically-directed growth. Systems capable of such behavior typically make use of "glue cooperation" in which the glues on at least $2$ sides of a tile must…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
In this paper, we work in a 2D version of the probabilistic variant of Winfree's abstract Tile Assembly Model defined by Chandran, Gopalkrishnan and Reif (SICOMP 2012) in which attaching tiles are sampled uniformly with replacement. First,…
Manually authoring 3D shapes is difficult and time consuming; generative models of 3D shapes offer compelling alternatives. Procedural representations are one such possibility: they offer high-quality and editable results but are difficult…
We extend previously known two-dimensional multiplication tiling systems that simulate multiplication by two natural numbers $p$ and $q$ in base $pq$ to higher dimensional multiplication tessellation systems. We develop the theory of these…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Protein assembly plays an important role throughout all phyla of life, both physiologically and pathologically. In particular, aggregation and polymerization of proteins are key-strategies that regulate cellular function. In recent years,…
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application…