Related papers: GC3 Biology in Eukaryotes and Prokaryotes
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
Recently we have extended our the "unified" model of evolutionary ecology to incorporate the {\it spatial inhomogeneities} of the eco-system and the {\it migration} of individual organisms from one patch to another within the same…
It now appears phenomenologically that the third family of fundamental fermions may be essentially different fron the first two. Particularly the high value (174GeV?) of the top quark mass suggests a special role. In the standard model all…
Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both…
This paper deals with branching processes in varying environment, namely, whose offspring distributions depend on the generations. We provide sufficient conditions for survival or extinction which rely only on the first and second moments…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
This talk presents recent calculations in full QCD of the lowest three moments of generalized parton distributions and the insight they provide into the behavior of nucleon electromagnetic form factors, the origin of the nucleon spin, and…
We pursue the investigation of a previously proposed correlation between chemical properties and physical evolutionary stage of isolated low-mass star-forming regions. In the past, the NH3/CCS abundance ratio was suggested to be a…
Despite tremendous advances in the field of genomics, the amount and function of the large non-coding part of the genome in higher organisms remains poorly understood. Here we report an observation, made for 37 fully sequenced eukaryotic…
We introduce generalized quark and gluon distributions in the deuteron, which can be measured in exclusive processes like deeply virtual Compton scattering and meson electroproduction. We discuss the basic properties of these distributions,…
The origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence,…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
This paper considers the behavior of discrete and continuous mathematical models for gene expression in the presence of transcriptional/translational bursting. We treat this problem in generality with respect to the distribution of the…
A motivation for studying the following problems comes from applications to Biology; see \cite{cifuentes20233d}. In the $3$-dimensional Euclidean space ${\bf{E}}^3$, fix six pairwise distinct points \begin{equation*} \label{eqA}…
An approach based on using the idea of distinguished coding phase in explicit form for identification of protein-coding regions (exons) in whole genome has been proposed. For several genomes an optimal window length for averaging GC-content…
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…
We aim to demonstrate the scientific potential of the Gaia Early Data Release 3 (EDR3) for the study of the Milky Way structure and evolution. We used astrometric positions, proper motions, parallaxes, and photometry from EDR3 to select…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
Hydrogen cations, or protons, provide the medium by which energy is stored and converted in biological systems. Such pre-eminence relies on the interplay between interfacial and bulk chemical transformations, according to mechanisms that…
Based on an Invited Plenary Talk given at ``Workshop on Physics and Experiments with Linear $e^+e^-$ Colliders,'' Waikoloa, Hawaii, April 26--30, 1993. This paper reviews theoretical issues concerning the structure of vector bosons, with…