Related papers: Further Thoughts on Abnormal Chromatin Configurati…
This paper provides a review of the variants of dark matter (CDM, HDM) which are thought to be fundamental components of the universe and their role in origin and evolution of structures.
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
We study the three-dimensional structure formation when atoms are deposited onto a substrate with a decagonal quasicrystalline order. Molecular-dynamicscalculations show that the adsorbate layer consists of ordered nano-scale domains with…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
Genes communicate with each other through different regulatory effects, which lead to the emergence of complex structures in cells, and such structures are expected to be different for normal and cancerous cells. To study breast cancer…
The role of neutrinos in big bang nucleosynthesis is discussed. The bounds on the number of neutrino families, neutrino degeneracy, parameters of neutrino oscillations are presented. A model of chemically inhomogeneous, while energetically…
Important aspects of the process of information storage and retrieval in DNA and RNA, and its evolution, are the role of the anticodons and associated $t$RNA's, and correlations between anticodons and amino acids; the degeneracy of the…
Most cancers in humans are large, measuring centimeters in diameter, composed of many billions of cells. An equivalent mass of normal cells would be highly heterogeneous as a result of the mutations that occur during each cell division.…
Several orders of magnitude typically separate the contour length of eukaryotic chromosomes and the size of the nucleus where they are confined. The ensuing topological constraints can slow down the relaxation dynamics of genomic filaments…
In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those…
We study quantum analogs of graph colorings and chromatic number. Initially defined via an interactive protocol, quantum colorings can also be viewed as a natural operator relaxation of graph coloring. Since there is no known algorithm for…
Adaptive Phase 2/3 designs hold great promise in contemporary oncology drug development, especially when limited data from Phase 1 dose-finding is insufficient for identifying an optimal dose. However, there is a general concern about…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…
This paper proposes a novel chaotic reaction-diffusion model of cellular tumor growth and metastasis. The model is based on the multiscale diffusion cancer-invasion model (MDCM) and formulated by introducing strong nonlinear coupling into…
We introduce a new computer aided detection and diagnosis system for lung cancer screening with low-dose CT scans that produces meaningful probability assessments. Our system is based entirely on 3D convolutional neural networks and…
The study of correlation structure in the primary sequences of DNA is reviewed. The issues reviewed include: symmetries among 16 base-base correlation functions, accurate estimation of correlation measures, the relationship between $1/f$…
Synthesizability remains a critical bottleneck in generative molecular design. While recent advances have addressed synthesizability in 2D graphs, extending these constraints to 3D for geometry-based conditional generation remains largely…
The study of exotic nuclei---nuclei with the ratio of neutron number $N$ to proton number $Z$ deviating much from that of those found in nature---is at the forefront of nuclear physics research because it can not only reveal novel nuclear…
This is an introduction to the special issue Genome organization: experiments and simulations, published in Chromosome Research, volume 25, issue 1 (2017).