Related papers: GC3 Biology in Eukaryotes and Prokaryotes
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
We investigate the distribution of flavonoids, a major category of plant secondary metabolites, across species. Flavonoids are known to show high species specificity, and were once considered as chemical markers for understanding adaptive…
We use detailed balance for a hadron composed of quark and gluon Fock states to obtain parton distributions in the proton and pion on the basis of a simple statistical model.
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
This paper discusses a selected part of the experimental program dedicated to the study of Generalized Parton Distributions, a recently introduced concept which provides a comprehensive framework for investigations of the partonic structure…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…
Saturation and geometrical scaling (GS) of gluon distributions are a consequence of the non-linear evolution equations of QCD. We argue that in pp GS holds for the inelastic cross-section rather than for the multiplicity distributions. We…
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
Nowadays, due to the increasing amount of experimental data obtained by sequencing, the most interest is focused on determining the functions and characteristics of its individual parts of the genome instead of determining the nucleotide…
The average size of internal translated exons, ranging from 120 to 165 nt across metazoans, is approximately the size of the typical mononucleosome (147 nt). Genome-wide study has also shown that nucleosome occupancy is significantly higher…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
In this paper we motivate and develop a model of gene expression for the purpose of studying the interaction between synthetic gene circuits and the chassis cell within which they are in- serted. This model focuses on the translational…
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal…
A primordial genetic code is proposed, having only four codons assigned, GGC meaning glycine, GAC meaning aspartate/glutamate, GCC meaning alanine-like and GUC meaning valine-like. Pathways of ambiguity reduction enlarged the codon…
The CTEQ program for the determination of parton distributions through a global QCD analysis of data for various hard scattering processes is fully described. A new set of distributions, CTEQ3, incorporating several new types of data is…
The outline of the presentation is as follows: I. Nucleon Distribution in the Deuteron from $e-D$ and $p-D$ Processes. II. Quark Distribution in Deuteron from its Fragmentation to Pions and Deep Inelastic $e-D$ scattering. III.Difference of…
As an extended and more complete version of the primary QCD nucleation model presented in Ref. [1], the new model introduces explicitly the transition balance and formulates it in both macroscopic and microscopic descriptions. The…
In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues…