Related papers: The entropic lock and key of the histone code
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
Accurate antenna affiliation identification is crucial for optimizing and maintaining communication networks. Current practice, however, relies on the cumbersome and error-prone process of manual tower inspections. We propose a novel…
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing…
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
Embryonic stem cells (ESC) have the potential to self-renew indefinitely and to differentiate into any of the three germ layers. The molecular mechanisms for self-renewal, maintenance of pluripotency and lineage specification are poorly…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…
High-order harmonic generation (HHG) is a powerful tool for probing electronic structure and ultrafast dynamics in matter. Traditionally studied in atomic and molecular gases, HHG has recently been extended to condensed matter, enabling…
We estimate by Monte Carlo simulations the configurational entropy of $N$-steps polygons in the cubic lattice with fixed knot type. By collecting a rich statistics of configurations with very large values of $N$ we are able to analyse the…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Topologically constrained genome-like polymers often double-fold into tree-like configurations. Here we calculate the exact number of tightly double-folded configurations available to a ring polymer in ideal conditions. For this purpose, we…
Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a…
Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
High-density phase change memory (PCM) storage is proposed for materials with multiple intermediate resistance states, which have been observed in 1$T$-TaS$_2$ due to charge density wave (CDW) phase transitions. However, the metastability…
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…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
Encoding data as a set of unordered strings is receiving great attention as it captures one of the basic features of DNA storage systems. However, the challenge of constructing optimal redundancy codes for this channel remained elusive. In…