Related papers: Shapes of interacting RNA complexes
Systematic relations between multiple objects that occur in various fields can be represented as networks. Real-world networks typically exhibit complex topologies whose structural properties are key factors in characterizing and further…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
The problem of RNA genomes packaged inside spherical viruses is studied. The viral capsid is modeled as a hollowed sphere. The attraction between RNA molecules and the inner viral capsid is assumed to be non-specific and occurs at the inner…
As a general type of machine learning approach, artificial neural networks have established state-of-art benchmarks in many pattern recognition and data analysis tasks. Among various kinds of neural networks architectures, polynomial neural…
In this study, we present a concept of morphing structure -- featuring an arch mounted on a compliant base -- that can be reconfigured via snap-through buckling and leverages bistability to retain its morphed shape. We show that…
We studied the formation of complex patterns using a variational principle and a standard energy functional. These patterns evolve by letting the system to search for the optimal configuration of a high conductivity channel, that in one…
Convolutional Neural Networks (CNNs) have recently led to incredible breakthroughs on a variety of pattern recognition problems. Banks of finite impulse response filters are learned on a hierarchy of layers, each contributing more abstract…
A method evaluating the sensitivity of a given parameter to topological changes is proposed within the method of moments paradigm. The basis functions are used as degrees of freedom which, when compared to the classical pixeling technique,…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
Ribonucleic Acid (RNA) can fold into shapes that perform functions in the cell. These foldings are governed by Watson-Crick base pairing, namely Adenine to Uracil and Cytosine to Guanine (A-U and G-C). The properties of the H-P…
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…
The representations learned by deep neural networks are difficult to interpret in part due to their large parameter space and the complexities introduced by their multi-layer structure. We introduce a method for computing persistent…
This article considers proximal planar shapes in terms of the proximity of shape nerves and shape nerve complexes. A shape nerve is collection of 2-simplexes with nonempty intersection on a triangulated shape space. A planar shape is a…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
RNA's diverse biological functions stem from its structural versatility, yet accurately predicting and designing RNA sequences given a 3D conformation (inverse folding) remains a challenge. Here, I introduce a deep learning framework that…
Molecular structures of RNA molecules reconstructed from X-ray crystallography frequently contain errors. Motivated by this problem we examine clustering on a torus since RNA shapes can be described by dihedral angles. A previously…
We address a long-standing problem in colloid and nanoparticle science: particle shape selection in solution synthesis. Our main finding is that a proper balance of two processes, preferential attachment of transported monomers at the…
Despite decades of effort, understanding the shape of genome space in biology remains a challenge due to the similarity, variability, diversity, and plasticity of evolutionary relationships among species, genes, or other biological…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…