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Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
We have developed a 3-D Monte Carlo radiative transfer model which computes line and continuum polarization variability for a binary system with an optically thick non-axisymmetric envelope. This allows us to investigate the complex…
Motif finding in DNA, RNA and proteins plays an important role in life science research. Recent patents concerning motif finding in the biomolecular data are recorded in the DNA Patent Database which serves as a resource for policy makers…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
Stern's diatomic sequence is a well-studied and simply defined sequence with many fascinating characteristics. The binary signed-digit (BSD) representation of integers is used widely in efficient computation, coding theory and other…
General matrix multiplication (GEMM) is the computational backbone of modern AI workloads, and its efficiency is critically dependent on effective tiling strategies. Conventional approaches employ symmetric tile buffering, where the…
We present a novel way to encode compositional information in high-dimensional (HD) vectors. Inspired by chromosomal crossover, random HD vectors are recursively interwoven, with a fraction of one vector's components masked out and replaced…
Electronic and magnetic properties of DNA structures doped by simple and transition d- and f-metal ions (Gd, La, Cu, Zn, Au) are reviewed. Both one- and two dimensional systems are considered. A particular attention is paid to gadolinium…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
Deep neural networks (DNN) have been used successfully in many scientific problems for their high prediction accuracy, but their application to genetic studies remains challenging due to their poor interpretability. In this paper, we…
Ordinary binary multiplication of natural numbers can be generalized in a non-trivial way to a ternary operation by considering discrete volumes of lattice hexagons. With this operation, a natural notion of `3-primality' -- primality with…
Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been…
Dielectric tensor tomography (DTT) enables the reconstruction of three-dimensional (3D) dielectric tensors, which provides a physical measure of 3D optical anisotropy. Herein, we present a cost-effective and robust method for DTT…
A phenomenological model based on the three-dimensional theory of nonlinear elasticity is developed to describe the phenomenon of overstretching in the force-extension curve for dsDNA. By using the concept of a material with multiple…
While binary neural networks (BNNs) offer significant benefits in terms of speed, memory and energy, they encounter substantial accuracy degradation in challenging tasks compared to their real-valued counterparts. Due to the binarization of…
A Triangle Generative Adversarial Network ($\Delta$-GAN) is developed for semi-supervised cross-domain joint distribution matching, where the training data consists of samples from each domain, and supervision of domain correspondence is…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
Synthesizing medical images while preserving their structural information is crucial in medical research. In such scenarios, the preservation of anatomical content becomes especially important. Although recent advances have been made by…