Related papers: Computing 3D chromatin configurations from contact…
Inspired by recent advances in the chromosome capture techniques, a method is proposed to study the structural organization of systems of polymers rings with topological constraints.To this purpose, the system is divided into compartments…
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
We investigate the large-scale geometry of the DNA-protein complex of chromatin using a generalized optimality principle, which requires that not only should all sub-parts of a natural process be optimal but also the unfolding of higher…
Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large data sets probing…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
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 mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three…
A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various…
We present an extension to the iterative Boltzmann inversion method to generate coarse-grained models with three-body intramolecular potentials that can reproduce correlations in structural distribution functions. The coarse-grained…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC…
Chromatin organization and dynamics is studied in this work at scales ranging from single nucleosome to nucleosomal array by using a unique combination of biochemical assays, single molecule imaging technique and numerical modeling. We…
In living cells, proteins involved in specialized biochemical functions are often spatially organized within biomolecular condensates. Increasing evidence suggests that some of these condensates, including DNA repair condensates, emerge…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
Recent research on accelerated gradient methods of use in optimization has demonstrated that these methods can be derived as discretizations of dynamical systems. This, in turn, has provided a basis for more systematic investigations,…
We demonstrate that inverse statistical mechanical optimization can be used to discover simple (e.g., short-range, isotropic, and convex-repulsive) pairwise interparticle potentials with three-dimensional diamond or simple cubic lattice…
Recent experiments on twisted bilayer graphene show the urgent need for establishing a low-energy lattice model for the system. We use the constrained random phase approximation to study the interaction parameters of such models taking into…
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…