Related papers: Single-Molecule Morphology of Topologically Digest…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
Two important tasks in the field of Topological Data Analysis are building practical multifiltrations on objects and using TDA to detect the geometry. Motivated by the tasks, we build multiparameter filtrations by operators on images named…
It is well-known that intrinsically disordered proteins (IDP) are highly dynamic, which is related to their functionality in various biological processes. However, the characterization of the intricate structures of IDP has been a…
Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
We consider the slow and athermal deformations of amorphous solids and show how the ensuing sequence of discrete plastic rearrangements can be mapped onto a directed network. The network topology reveals a set of highly connected regions…
The human organism is an integrated network where complex physiologic systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Identifying and…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
Topological entanglements are abundant, and often detrimental, in polymeric systems in biology and materials science. Here we theoretically investigate the topological simplification of knots by diffusing slip-links (SLs), which may…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
The automated segmentation of cancer tissue in histopathology images can help clinicians to detect, diagnose, and analyze such disease. Different from other natural images used in many convolutional networks for benchmark, histopathology…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is…
As a granular material is compressed, the particles and forces within the system arrange to form complex heterogeneous structures. Force chains are a prime example and are thought to constrain bulk properties such as mechanical stability…
Brain plasticity, also known as neuroplasticity, is a fundamental mechanism of neuronal adaptation in response to changes in the environment or due to brain injury. In this review, we show our results about the effects of synaptic…
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish…
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…
We present results relevant to the equilibrium organization of DNA strands of arbitrary length interacting with a spherical organizing center, suggestive of DNA-histone complexation in nucleosomes. We obtain a rich phase diagram in which a…
Multiplex networks are convenient mathematical representations for many real-world -- biological, social, and technological -- systems of interacting elements, where pairwise interactions among elements have different flavors. Previous…
This work deals with the construction of networks of topological defects in models described by a single complex scalar field. We take advantage of the deformation procedure recently used to describe kinklike defects in order to build…
Cytoskeletons are self organized networks based on polymerized proteins, actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality…