Related papers: Dynamic cluster-scaling in DNA
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
Clustering aims to group unlabeled objects based on similarity inherent among them into clusters. It is important for many tasks such as anomaly detection, database sharding, record linkage, and others. Some clustering methods are taken as…
Discrete mixture models provide a well-known basis for effective clustering algorithms, although technical challenges have limited their scope. In the context of gene-expression data analysis, a model is presented that mixes over a finite…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
Well-calibrated scaling relations between the observable properties and the total masses of clusters of galaxies are important for understanding the physical processes that give rise to these relations. They are also a critical ingredient…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility (JLab), clustering aspects are studied in structure functions of deep inelastic…
It appears that the dynamical status of clusters and groups of galaxies is related to the large-scale structure of the Universe. A few interesting trends have been established: (1) The Cluster Substructure - Alignment Connection, by which…
Colloidal gels formed by strongly attractive particles at low particle volume fractions are composed of space-spanning networks of uniformly sized clusters. We study the thermal fluctuations of the clusters using differential dynamic…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
Spectral clustering is a fast and popular algorithm for finding clusters in networks. Recently, Chaudhuri et al. (2012) and Amini et al.(2012) proposed inspired variations on the algorithm that artificially inflate the node degrees for…
X-ray images of galaxy clusters often show disturbed structures that are indication of cluster mergers. As a complementary to our previous work on dynamical state of 964 clusters observed by the Chandra, we process the X-ray images for 1308…
Bi-clustering is a useful approach in analyzing biological data when observations come from heterogeneous groups and have a large number of features. We outline a general Bayesian approach in tackling bi-clustering problems in moderate to…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
We present a new algorithm for clustering longitudinal data. Data of this type can be conceptualized as consisting of individuals and, for each such individual, observations of a time-dependent variable made at various times. Generically,…
Spontaneous formation of clusters of synchronized spiking in a structureless ensemble of equal stochastically perturbed excitable neurons with delayed coupling is demonstrated for the first time. The effect is a consequence of a subtle…
A hierarchical scheme for clustering data is presented which applies to spaces with a high number of dimension ($N_{_{D}}>3$). The data set is first reduced to a smaller set of partitions (multi-dimensional bins). Multiple clustering…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
Statistical aspects of the dynamics of chaotic scattering in the classical model of $\alpha$-cluster nuclei are studied. It is found that the dynamics governed by hyperbolic instabilities which results in an exponential decay of the…
The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two probability functions describing coherently localized…