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Wall-clock-time is minimized for a solution to a linear-program with block-diagonal-structure, by decomposing the linear-program into as many small-sized subproblems as possible, each block resulting in a separate subproblem, when the…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Discrete tomography deals with reconstructing finite spatial objects from lower dimensional projections and has applications for example in timetable design. In this paper we consider the problem of reconstructing a tile packing from its…
Mining and exploring databases should provide users with knowledge and new insights. Tiles of data strive to unveil true underlying structure and distinguish valuable information from various kinds of noise. We propose a novel Boolean…
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and…
Self-assembly is a fundamental concept in biology and of significant interest to nanotechnology. Significant progress has been made in characterizing and controlling the properties of the resulting structures, both experimentally and…
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…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
Consistency distillation methods have demonstrated significant success in accelerating generative tasks of diffusion models. However, since previous consistency distillation methods use simple and straightforward strategies in selecting…
We study the problem of determining whether a given temporal specification can be implemented by a symmetric system, i.e., a system composed from identical components. Symmetry is an important goal in the design of distributed systems,…
Self-assembly of nanoscale synthetic subunits is a promising bottom-up strategy for fabrication of functional materials. Here, we introduce a design principle for DNA origami nanoparticles of 50-nm size, exploiting modularity, to make a…
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
We show that in the hierarchical tile assembly model, if there is a producible assembly that overlaps a nontrivial translation of itself consistently (i.e., the pattern of tile types in the overlap region is identical in both translations),…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
Advances in life sciences over the last few decades have lead to the generation of a huge amount of biological data. Computing research has become a vital part in driving biological discovery where analysis and categorization of biological…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
Recently, methodology was presented to facilitate the incorporation of interim analyses in stepped-wedge (SW) cluster randomised trials (CRTs). Here, we extend this previous discussion. We detail how the stopping boundaries, allocation…
Consecutive matrix multiplications are commonly used in graph neural networks and sparse linear solvers. These operations frequently access the same matrices for both reading and writing. While reusing these matrices improves data locality,…