Related papers: Algorithmic Self-Assembly of DNA Tiles and its App…

The cryptanalysis of various cipher problems can be formulated as NP-Hard combinatorial problem. Solving such problems requires time and/or memory requirement which increases with the size of the problem. Techniques for solving…

Large-degree polynomial multiplication is an integral component of post-quantum secure lattice-based cryptographic algorithms like CRYSTALS-Kyber and Dilithium. The computational complexity of large-degree polynomial multiplication can be…

Deep neural networks have proven to be quite effective in a wide variety of machine learning tasks, ranging from improved speech recognition systems to advancing the development of autonomous vehicles. However, despite their superior…

Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…

DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…

Data storage is one of the main computing issues of this century. Not only storage devices are converging to strict physical limits, but also the amount of data generated by users is growing at an unbelievable rate. To face these…

Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly 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…

Deep learning (DL) has shown unprecedented performance for many image analysis and image enhancement tasks. Yet, solving large-scale inverse problems like tomographic reconstruction remains challenging for DL. These problems involve…

DNA origami is a widely used method to construct nanostructures by self-assembling designed DNA strands. These structures are often used as "pegboards" for templated assembly of proteins, gold nanoparticles, aptamers, and other molecules,…

Self-organized complex structures in nature, e.g. viral capsids, hierarchical biopolymers, and bacterial flagella, offer efficiency, adaptability, robustness, and multi-functionality. Can we program the self-assembly of three-dimensional…

Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…

DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…

DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…

The algorithms in the current sequential numerical linear algebra libraries (e.g. LAPACK) do not parallelize well on multicore architectures. A new family of algorithms, the tile algorithms, has recently been introduced. Previous research…

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…

Clustering algorithms remain valuable tools for grouping and summarizing the most important aspects of data. Example areas where this is the case include image segmentation, dimension reduction, signals analysis, model order reduction,…

We consider the problem of reconstructing graphs or labeled graphs from neighborhoods of a given radius r. Special instances of this problem include the well known: DNA shotgun assembly; the lesser-known: neural network reconstruction; and…

DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…

Controlled synthesis of materials with specified atomic structures underpins technological advances yet remains reliant on iterative, trial-and-error approaches. Nanoparticles (NPs), whose atomic arrangement dictates their emergent…