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Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
Non-periodic folding of periodic crease patterns paves the way to novel nonlinear phenomena that cannot be feasible through periodic folding. This paper focuses on the non-periodic folding of recursive crease patterns generalized from…
Genetic oscillators are present in the cells of many organisms and control several biological processes. The common feature of such oscillators is the presence of a protein which represses the transcription of its own gene. Recently, it has…
Bootstrap percolation on a graph iteratively enlarges a set of occupied sites by adjoining points with at least $\theta$ occupied neighbors. The initially occupied set is random, given by a uniform product measure, and we say that spanning…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large…
We survey recent developments in fractal analysis of regular and slow-fast dynamical systems using Minkowski dimension. Our focus is on spiral trajectories near monodromic limit periodic sets in regular systems and entry-exit sequences in…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
Band structure unfolding is a key technique for analyzing and simplifying the electronic band structure of large, internally distorted supercells that break the primitive cell's translational symmetry. In this work, we present an efficient…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
Motivated by the problem of determining unknotted routes for the scaffolding strand in DNA origami self-assembly, we examine existence and knottedness of A-trails in graphs embedded on the torus. We show that any A-trail in a…
In topology, a torus remains invariant under certain non-trivial transformations known as modular transformations. In the context of topologically ordered quantum states of matter, these transformations encode the braiding statistics and…
We extend the quandle cocycle invariant to the context of stuck links. More precisely, we define an invariant of stuck links by assigning Boltzmann weights at both classical and stuck crossings. As an application, we define a…
Quantum oracles are widely adopted in problems, like query oracle in Grover's algorithm, cipher in quantum cryptanalytic and data encoder in quantum machine learning. Notably, the bit-flip oracle, capable of flipping the state based on a…
We propose a dynamical model in which a network structure evolves in a self-organized critical (SOC) manner and explain a possible origin of the emergence of fractal and small-world networks. Our model combines a network growth and its…
Kernel matrices (e.g. Gram or similarity matrices) are essential for many state-of-the-art approaches to classification, clustering, and dimensionality reduction. For large datasets, the cost of forming and factoring such kernel matrices…
Estimating a fractal dimension from a finite stochastic trajectory is a finite-size scaling problem: the apparent box-counting exponent is shaped by an occupancy crossover between the resolved range of scales and the finite number of…
In this paper, a simple dynamical model in which fractal networks are formed by self-organized critical (SOC) dynamics is proposed; the proposed model consists of growth and collapse processes. It has been shown that SOC dynamics are…
The self-similarity properties of fractals are studied in the framework of the theory of entire analytical functions and the $q$-deformed algebra of coherent states. Self-similar structures are related to dissipation and to noncommutative…