Related papers: Cluster-scaling, chaotic order and coherence in DN…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
Collective behavior is studied in globally coupled maps with distributed nonlinearity. It is shown that the heterogeneity enhances regularity in the collective dynamics. Low-dimensional quasiperiodic motion is often found for the…
Effect of noise in inducing order on various chaotically evolving systems is reviewed, with special emphasis on systems consisting of coupled chaotic elements. In many situations it is observed that the uncoupled elements when driven by…
Clustering genotypes based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of…
We report the phenomenon of frequency clustering in a network of Hodgkin-Huxley neurons with spike timing-dependent plasticity. The clustering leads to a splitting of a neural population into a few groups synchronized at different…
The ability of cells to reorganize in response to external stimuli is important in areas ranging from morphogenesis to tissue engineering. Elongated cells can co-align due to steric effects, forming states with local order. We show that…
We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
Many networked systems are governed by non-pairwise interactions between nodes. The resulting higher-order interaction structure can then be encoded by means of a hypernetwork. In this paper we consider dynamical systems on hypernetworks by…
Mixture model-based frameworks are very popular for statistical inference in clustering. While convenient for producing probabilistic estimates of cluster assignments and uncertainty, they are prone to misspecification, which can lead to…
The theory of phase ordering dynamics -- the growth of order through domain coarsening when a system is quenched from the homogeneous phase into a broken-symmetry phase -- is reviewed, with the emphasis on recent developments. Interest will…
We investigate the influence of morphology and size on the vibrational properties of disordered clusters of colloidal particles with attractive interactions. From measurements of displacement correlations between particles in each cluster,…
A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…
Chaos is associated with stochasticity, complex, irregular motion, etc. It has some peculiar properties such as ergodicity, highly initial value sensitivity, non-periodicity and long-term unpredictability. These pseudo random features lead…
Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical…
We propose a new method for determining the stochastic or ordered nature of trajectories in non-integrable Hamiltonian dynamical systems. The method consists of constructing a time-series from the divergence of nearby trajectories and then…
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A…
We propose a new procedure for clustering nucleotide sequences based on the "Laplacian Eigenmaps" and Gaussian Mixture modelling. This proposal is then applied to a set of 100 DNA sequences from the mitochondrially encoded NADH…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…