Related papers: Dynamic cluster-scaling in DNA
The coagulation of dust particles is a key process in planetesimal formation. However, the radial drift and bouncing barriers are not completely resolved, especially for silicate dust. Since the collision velocities of dust particles are…
Many natural and engineered complex networks have intricate mesoscopic organization, e.g., the clustering of the constituent nodes into several communities or modules. Often, such modularity is manifested at several different hierarchical…
Biologists have long observed periodic-like oxygen consumption oscillations in yeast populations under certain conditions and several unsatisfactory explanations for this phenomenon have been proposed. These "autonomous oscillations" have…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
The community structure of complex networks reveals both their organization and hidden relationships among their constituents. Most community detection methods currently available are not deterministic, and their results typically depend on…
Soft-granular media, such as dense emulsions, foams or tissues, exhibit either fluid- or solid-like properties depending on the applied external stresses. Whereas bulk rheology of such materials has been thoroughly investigated, the…
According to microscopic calculations with antisymmetrized molecular dynamics, we studied cluster features in stable and unstable nuclei. A variety of structure was found in stable and unstable nuclei in the $p$-shell and $sd$-shell…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
Deterministic simulations of the rate equations governing cluster dynamics in materials are limited by the number of equations to integrate. Stochastic simulations are limited by the high frequency of certain events. We propose a coupling…
We investigate experimentally the connection between short time dynamics and long time dynamical heterogeneities within a dense granular media under cyclic shear. We show that dynamical heterogeneities result from a two timescales process.…
Star clusters - open and globulars - experience dynamical evolution on time scales shorter than their age. Consequently, open and globular clusters provide us with unique dynamical laboratories for learning about two-body relaxation, mass…
When multivalent salts are added to dilute DNA solution, the DNA chains condense into bundles of a well-defined size. We explore two physical problems motivated by this phenomenon: the origin of the attractive interactions between the…
We derive exact equations for the spectral density of sparse networks with an arbitrary distribution of the number of single edges and triangles per node. These equations enable a systematic investigation of the effect of clustering on the…
Using molecular dynamics simulation, we investigate the slow dynamics of a supercooled binary mixture of soft particles interacting with a generalized Hertzian potential. At low density, it displays typical slow dynamics near its glass…
Studies of nucleation generally focus on the properties of the critical cluster, but the presence of defects within the crystal lattice means that the population of nuclei necessarily evolve through a distribution of pre-critical clusters…
We study the collective behaviour of an ensemble of coupled motile elements whose interactions depend on time and are alternatively attractive or repulsive. The evolution of interactions is driven by individual internal variables with…
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…
DNA self-assembly is a well-understood nanotechnology to obtain extremely ordered structures from the nanometer to up to the hundred of microns scale. By contrast, DNA hydrogels rely on the disordered assembly of DNA building blocks to…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…