Related papers: Statistics of topological RNA structures
Recent genomic and bioinformatic advances have motivated the development of numerous random network models purporting to describe graphs of biological, technological, and sociological origin. The success of a model has been evaluated by how…
We analyze the structure of two dimensional disordered cellular systems generated by extensive computer simulations. These cellular structures are studied as topological trees rooted on a central cell or as closed shells arranged…
The theory of $G$-structures provides us with a unified framework for a large class of geometric structures, including symplectic, complex and Riemannian structures, as well as foliations and many others. Surprisingly, contact geometry -…
Understanding the base pairing of an RNA sequence provides insight into its molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes…
Understanding the biological function of knots in proteins and their folding process is an open and challenging question in biology. Recent studies classify the topology and geometry of knotted proteins by analysing the distribution of a…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
Evolutionary mechanism in a self-organized system cause some functional changes that force to adapt new conformation of the interaction pattern between the components of that system. Measuring the structural differences one can retrace the…
We study the richness of the ensemble of graphical structures (i.e., unlabeled graphs) of the one-dimensional random geometric graph model defined by $n$ nodes randomly scattered in $[0,1]$ that connect if they are within the connection…
In this paper we study canonical $\gamma$-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $\gamma$-structure is composed by specific building…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
We consider the dynamics of a reaction-diffusion system on a multigraph. The species share the same set of nodes but can access different links to explore the embedding spatial support. By acting on the topology of the networks we can…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA…
One property of networks that has received comparatively little attention is hierarchy, i.e., the property of having vertices that cluster together in groups, which then join to form groups of groups, and so forth, up through all levels of…
We study low-dimensional problems in topology and geometry via a study of contact and Cauchy-Riemann ($CR$) structures. A contact structure is called spherical if it admits a compatible spherical $CR$ structure. We will talk about spherical…
The observation, design and analysis of mesh-like networks in bionics, polymer physics and biological systems has brought forward an extensive catalog of fascinating structures of which a subgroup share a particular, yet critically under…
We explore the interplay between the topological relevance of a neuron and its dynamical traces in experimental cultured neuronal networks. We monitor the growth and development of these networks to characterise the evolution of their…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
In this paper, we study some topological characteristics of the n-normed spaces. We observe convergence sequences, closed sets, and bounded sets in the n-normed spaces using norms of quotient spaces that will be constructed. These norms…