Related papers: From Effective Interactions Extracted Using Hi-C D…
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance…
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
In this work, the intermeson interactions of double-beauty $\bar{B}\bar{B}$, $\bar{B}\bar{B}^\ast$, and $\bar{B}^\ast\bar{B}^\ast$ systems have been studied with heavy meson chiral effective field theory. The effective potentials are…
Effective interactions can be obtained from a renormalization group analysis in two complementary ways. One can either explicitly integrate out higher energy modes or impose given conditions at low energies for a cut-off theory. While the…
Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a…
Hi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…
I explore the form of the effective interaction in harmonic-oscillator-based effective theory (HOBET) in next-to-next-to-next-to-leading order (N3LO). As the included space in a HOBET (as in the shell model) is defined by the oscillator…
The phase diagram of the attractive Hubbard model with spatially inhomogeneous interactions is obtained using a single site dynamical mean field theory like approach. The model is characterized by three parameters: the interaction strength,…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
The three-dimensional organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state - accessibility and the amount of gene expression - of the chromatin. Recent advances in chromosome…
Results of an exploratory study of the antinucleon-nucleon interaction within chiral effective field theory are reported. The antinucleon-nucleon potential is derived up to next-to-next-to-leading order, based on a modified Weinberg power…
We construct valence-space Hamiltonians for use in shell-model calculations, where the residual two-body interaction is based on symmetry principles and the low-momentum expansion from chiral effective field theory. In addition to the usual…
An effective interaction is derived for use in the full pf basis. Starting from a realistic G-matrix interaction, 195 two-body matrix elements and 4 single-particle energies are determined by fitting to 699 energy data in the mass range 47…
We derive formulae for the electrostatic interaction between two long, rigid macromolecules that may have arbitrary surface charge patterns and cross at an arbitrary interaxial angle. We calculate the dependence of the interaction energy on…
We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics…