Related papers: Characterizing large scale base composition struct…
In systems biology, it is common to measure biochemical entities at different levels of the same biological system. One of the central problems for the data fusion of such data sets is the heterogeneity of the data. This thesis discusses…
In systems biology, it is becoming increasingly common to measure biochemical entities at different levels of the same biological system. Hence, data fusion problems are abundant in the life sciences. With the availability of a multitude of…
We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination…
Many materials, processes, and structures in science and engineering have important features at multiple scales of time and/or space; examples include biological tissues, active matter, oceans, networks, and images. Explicitly extracting,…
The standard model of large scale structure is considered, in which the structure originates as a Gaussian adiabatic density perturbation with a nearly scale invariant spectrum. The basic theoretical tool of cosmological perturbation theory…
We discuss correlation properties of a general mass density field introducing a classification of structures based on their complexity. Standard cosmological models for primordial mass fluctuations are characterized by a sort of large-scale…
The spatial distribution of DNA base sequence A, C, G and T exhibit selfsimilar fractal fluctuations and the corresponding power spectra follow inverse power law form, which implies the following: (1) A scale invariant eddy continuum,…
Spatial fluctuations of guanine and cytosine base content (GC%) are studied by spectral analysis for the complete set of human genomic DNA sequences. We find that (i) the 1/f^alpha decay is universally observed in the power spectra of all…
In this paper we treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping DNA sequences to integer sequences, followed by R/S analysis of the model and…
Hyperuniform many-body systems in $d$-dimensional Euclidean space are characterized by completely suppressed (normalized) infinite-wavelength density fluctuations, and appear to be endowed with novel exotic physical properties. In this…
Although theories regarding the role of sequence-specific DNA resonance in biology have abounded for over 40 years, the published evidence for it is lacking. Here, the authors reasoned that for sustained resonance signaling, the number of…
We study a scenario for the very early universe in which there is a fast phase transition from a non-geometric, high temperature phase to a low temperature, geometric phase described by a classical solution to the Einstein equations. In…
In this paper the question about statistical properties of block--hierarchical random matrices is raised for the first time in connection with structural characteristics of random hierarchical networks obtained by mipmapping procedure. In…
An idea to analyze the fluctuational mode or/and spectrum of water molecules in an inhomogeneous environment around a biomolecule such as protein and DNA is proposed based on the generalized Langevin equation (GLE) for water interacting…
The human genome contains repetitive DNA at different level of sequence length, number and dispersion. Highly repetitive DNA is particularly rich in homo-- and di--nucleotide repeats, while middle repetitive DNA is rich of families of…
In a class of heterogeneous random networks, where each node dynamics is a random dynamical system, interacting with neighbor nodes via a random coupling function, we characterize the hub behavior as the mean-field, subject to statistically…
Using a well defined soft model glass in the framework of Molecular Dynamics simulations, the inherent structures are probed by means of a recently developed deformation protocol that aims to capture the Dynamical Heterogeneities (DH), as…
We applied coherence analysis to molecular dynamics simulations of the plant protein crambin, a thionin storage protein found in Abyssinian cabbage. Coherence analysis was developed by engineers to identify linear interactions, without…
We develop a picture of dipole-nucleus (namely dilute-dense) and dipole-dipole (dilute-dilute) scattering in the high-energy regime based on the analysis of the fluctuations in the quantum evolution. We emphasize the difference in the…
Granular simulations are used to probe the particle scale dynamics at short, intermediate, and long time scales for gravity driven, dense granular flows down an inclined plane. On approach to the angle of repose, where motion ceases, the…