Related papers: Information-theoretic View of Sequence Organizatio…
In our previous publication [Kogan et al, Phys. Rev. {\bf 48}, 9404 (1993)] we considered the issue of statistics of radiation diffusively propagating in a disordered medium. The consideration was in the framework of diagrammatic techniques…
A methodology is developed to identify, as units of study, each decrease in the value of a stock from a given maximum price level. A critical level in the amount of price declines is found to separate a segment operating under a random walk…
Longevity of a taxonomic group is an important issue in understanding the dynamics of evolution. In this respect a key observation is that genera, families or orders can each be assigned a characteristic average lifetime [Van Valen, L.,…
Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…
Slow fluctuations of a qubit frequency are one of the major problems faced by quantum computers. To understand their origin it is necessary to go beyond the analysis of their spectra. We show that characteristic features of the fluctuations…
The information entropies in coordinate and momentum spaces and their sum ($S_r$, $S_k$, $S$) are evaluated for many nuclei using "experimental" densities or/and momentum distributions. The results are compared with the harmonic oscillator…
We present a theoretical framework that extends classical information theory to finite and structured systems by redefining redundancy as a fundamental property of information organization rather than inefficiency. In this framework,…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
In one dimensional wires, fluctuations destroy superconducting long-range order and stiffness at finite temperatures; in an infinite wire, quasi-long range order and stiffness survive at zero temperature if the wire's dimensionless…
We report a theoretical investigation on conductance fluctuation of mesoscopic systems. Extensive numerical simulations on quasi-one dimensional, two dimensional, and quantum dot systems with different symmetries (COE, CUE, and CSE)…
This paper establishes formal mathematical foundations linking Chaos Game Representations (CGR) of DNA sequences to their underlying $k$-mer frequencies. We prove that the Frequency CGR (FCGR) of order $k$ is mathematically equivalent to a…
This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences.…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
Statistical mechanics determines the abundance of different arrangements of matter depending on cost-benefit balances. Its formalism and phenomenology percolate throughout biological processes and set limits to effective computation. Under…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Bacterial genomes and large-scale computer software projects both consist of a large number of components (genes or software packages) connected via a network of mutual dependencies. Components can be easily added or removed from individual…
In quantum transport through nanoscale devices, fluctuations arise from various sources: the discreteness of charge carriers, the statistical non-equilibrium that is required for device operation, and unavoidable quantum uncertainty. As…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
We calculate the system-size-over-wave-length ($M$) dependence of sample-to-sample conductance fluctuations, using the open kicked rotator to model chaotic scattering in a ballistic quantum dot coupled by two $N$-mode point contacts to…