Related papers: Dynamic cluster-scaling in DNA
Knowledge on nuclear cluster physics has increased considerably as nuclear clustering remains one of the most fruitful domains of nuclear physics, facing some of the greatest challenges and opportunities in the years ahead. The occurrence…
We numerically study stochastic resonance in the unzipping of a model double-stranded DNA by a periodic force. We observe multiple peaks in stochastic resonance in the output signal as the driving force frequency is varied for different…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
Globular clusters are stellar dynamical systems which evolve on stellar evolutionary and both internal and external dynamical timescales. Quantitative comparison of cluster properties with realistic evolutionary dynamical models is becoming…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
Classification and clustering have been studied separately in machine learning and computer vision. Inspired by the recent success of deep learning models in solving various vision problems (e.g., object recognition, semantic segmentation)…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Coagulation-fragmentation processes describe the stochastic association and dissociation of particles in clusters. Cluster dynamics with cluster-cluster interactions for a finite number of particles has recently attracted attention…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
According to the experimental evidence damage induced by densely ionizing radiation in mammalian cells is distributed along the DNA molecule in the form of clusters. The most critical constituent of DNA damage are double-strand breaks…
Mixtures of active and passive particles are predicted to exhibit a variety of nonequilibrium phases. Here we report a dynamic clustering phase in mixtures of colloids and motile bacteria. We show that colloidal clustering results from a…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
We consider the problem of clustering nested or hierarchical data, where observations are grouped and there are both group-level and observation-level variables. In our motivating OneK1K dataset, observations consist of single-cell…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with $10^9$ atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
The description of complex configuration is a difficult issue. We present a powerful technique for cluster identification and characterization. The scheme is designed to treat with and analyze the experimental and/or simulation data from…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…