Related papers: Dynamic cluster-scaling in DNA
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
We review some recent work on the synchronization of coupled dynamical systems on a variety of networks. When nodes show synchronized behaviour, two interesting phenomena can be observed. First, there are some nodes of the floating type…
Two new criteria, that involve the microscopic dynamics of the system, are proposed for the identification of clusters in continuum systems. The first one considers a residence time in the definition of the bond between pairs of particles,…
We present a Molecular Dynamics study of large Lennard-Jones clusters evolving on a crystalline surface. The static and the dynamic properties of the cluster are described. We find that large clusters can diffuse rapidly, as experimentally…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
Motivated by theoretical advancements in dimensionality reduction techniques we use a recent model, called Block Markov Chains, to conduct a practical study of clustering in real-world sequential data. Clustering algorithms for Block Markov…
Bacteria suspension exhibits a wide range of collective phenomena arising from interactions between individual cells. Here we show Serratia marcescens cells near an air-liquid interface spontaneously aggregate into dynamic clusters through…
Cluster growth in a coagulating system of active particles (such as microswimmers in a solvent) is studied by theory and simulation. In contrast to passive systems, the net velocity of a cluster can have various scalings dependent on the…
We review recent work that investigates the formation of stellar clusters, ranging in scale from globular clusters through open clusters to the small scale aggregates of stars observed in T associations. In all cases, recent advances in…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
In this contribution, I will discuss two topics related to the clustering of atomic nuclei. The first is dual character of the ground state. Recently, it was pointed out that the ground states of atomic nuclei have dual character of shell…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and…
The network approach plays a distinguished role in contemporary science of complex systems/phenomena. Such an approach has been introduced into seismology in a recent work [S. Abe and N. Suzuki, Europhys. Lett. 65, 581 (2004)]. Here, we…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…