Related papers: Dynamic cluster-scaling in DNA
The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry,…
Over recent years, molecular simulations have provided invaluable insights into the microscopic processes governing the initial stages of crystal nucleation and growth. A key aspect that has been observed in many different systems is the…
In this paper we present the results of two detailed N-body simulations of the interaction of a sample of four massive globular clusters in the inner region of a triaxial galaxy. A full merging of the clusters takes place, leading to a…
The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to…
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the…
Clustering analysis identifies samples as groups based on either their mutual closeness or homogeneity. In order to detect clusters in arbitrary shapes, a novel and generic solution based on boundary erosion is proposed. The clusters are…
Motivated by DNA-based storage, we study the noisy shuffling channel, which can be seen as the concatenation of a standard noisy channel (such as the BSC) and a shuffling channel, which breaks the data block into small pieces and shuffles…
The formation of galaxy clusters in hierarchically clustering universes is investigated by means of high resolution N-body simulations. The simulations are performed using a newly developed multi-mass scheme which combines a PM code with a…
Clustering plays an important role in the structure of nuclei, especially for light nuclei in the $p$-shell. In nuclear cluster models these degrees of freedom are introduced explicitly. In the Resonating Group Method or in the Generator…
Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
Strongly correlated many-body systems often display the emergence of simple patterns and regular behaviour of their global properties. Phenomena such as clusterization, collective motion and appearance of shell structures are commonly…
A general theory of nucleation for colloids and macromolecules in solution is formulated within the context of fluctuating hydrodynamics. A formalism for the determination of nucleation pathways is developed and stochastic differential…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
In many cellular signaling pathways, key components form clusters at the cell membrane. Although much work has focused on the mechanisms behind such cluster formation, the implications for downstream signaling remain poorly understood.…
Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in…
Biomolecular condensates form by phase separation of biological polymers and have important functions in the cell $-$ functions that are inherently connected to their physical properties. A remarkable aspect of such condensates is that…