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This paper is dealing with DNA cyclic codes which play an important role in DNA computing and have attracted a particular attention in the literature. Firstly, we introduce a new family of DNA cyclic codes over the ring…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…
In this article, we completely classify torus bundles over the circle that bound 4-manifolds with the rational homology of the circle. Along the way, we classify certain integral surgeries along chain links that bound rational homology…
Dominant sequence models like the Transformer represent structure implicitly through dense attention weights, incurring quadratic complexity. We propose RewriteNets, a novel neural architecture built on an alternative paradigm: explicit,…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
The conformation of circular DNA molecules of various lengths adsorbed in a 2D conformation on a mica surface is studied. The results confirm the conjecture that the critical exponent $\nu$ is topologically invariant and equal to the SAW…
We give necessary conditions of a surface-knot to be ribbon concordant to another, by introducing a new variant of the cocycle invariant of surface-knots in addition to using the invariant already known. We demonstrate that twist-spins of…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
This PhD thesis is devoted to show that differential renormalization is a simple and useful renormalization method that we can use when dealing with gauge theories. In this work, it is shown how the one-loop results of Constraint…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. We have created a method for…
Our goal is to one day take a photo of a knot and have a phone automatically recognize it. In this expository work, we explain a strategy to approximate this goal, using a mixture of modern machine learning methods (in particular…
In the note we study Legendrian and transverse knots in rationally null-homologous knot types. In particular we generalize the standard definitions of self-linking number, Thurston-Bennequin invariant and rotation number. We then prove a…
We determine which integral surgeries on a large class of circular chain links bound rational homology balls. Our key tool is the lattice-theoretic cubiquity obstruction recently developed by Greene and Owens. We discuss a practical method…
Knotted molecules occur naturally and are designed by scientists to gain special biological and material properties. Understanding and utilizing knotting require efficient methods to recognize and generate knotted structures, which are…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
Prostate gland segmentation from T2-weighted MRI is a critical yet challenging task in clinical prostate cancer assessment. While deep learning-based methods have significantly advanced automated segmentation, most conventional…
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes…