Related papers: Posets and spaces of $k$-noncrossing RNA Structure…
Shape graphs are complex geometrical structures commonly found in biological and anatomical systems. A shape graph is a collection of nodes, some connected by curvilinear edges with arbitrary shapes. Their high complexity stems from the…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
Let $\Delta$ denote a non-degenerate $k$-simplex in $\mathbb{R}^k$. The set $\text{Sim}(\Delta)$ of simplices in $\mathbb{R}^k$ similar to $\Delta$ is diffeomorphic to $O(k)\times [0,\infty)\times \mathbb{R}^k$, where the factor in $O(k)$…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
Carbon nanotubes and biological filaments each spontaneously assemble into kinked helices, rings, and "tennis racket" shapes due to competition between elastic and interfacial effects. We show that the slender geometry is a more important…
Motivation coming from the study of affine Weyl groups, a structure of ranked poset is defined on the set of circular permutations in $S_n$ (that is, $n$-cycles). It is isomorphic to the poset of so-called admitted vectors, and to an…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
Branching architecture characterizes numerous systems, ranging from synthetic (hyper)branched polymers and biomolecules such as lignin, amylopectin, and nucleic acids to tracheal and neuronal networks. Its ubiquity reflects the many…
Biological functions of RNAs are determined by their three-dimensional (3D) structures. Thus, given the limited number of experimentally determined RNA structures, the prediction of RNA structures will facilitate elucidating RNA functions…
RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
We consider the topology of real no $k$-equal spaces via the theory of cellular spanning trees. Our main theorem proves that the rank of the $(k-2)$-dimensional homology of the no $k$-equal subspace of $\mathbb{R}$ is equal to the number of…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
Genes communicate with each other through different regulatory effects, which lead to the emergence of complex structures in cells, and such structures are expected to be different for normal and cancerous cells. To study breast cancer…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…