Related papers: Computing 3D chromatin configurations from contact…
Very soft grain assemblies have unique shape-changing capabilities that allow them to be compressed far beyond the rigid jammed state by filling void spaces more effectively. However, accurately following the formation of these systems by…
Recent experiments showing scaling of the intrachromosomal contact probability, $P(s)\sim s^{-1}$ with the genomic distance $s$, are interpreted to mean a self-similar fractal-like chromosome organization. However, scaling of $P(s)$ varies…
Given native 2D contact map, protein 3D structure could be reconstructed with accuracy of 2A or better, and such reconstruction is a feasible computational approach for protein folding problem. The prediction accuracy from traditional…
Apart from being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. The detailed knowledge of this code contrasts the…
This contribution proposes the first 3D beam-to-beam interaction model for molecular interactions between curved slender fibers undergoing large deformations. While the general model is not restricted to a specific beam formulation, in the…
Simulation of contact and friction dynamics is an important basis for control- and learning-based algorithms. However, the numerical difficulties of contact interactions pose a challenge for robust and efficient simulators. A…
Topologically stabilized polymer conformations observed in melts of nonconcatenated polymer rings and crumpled globules, are considered to be a good candidate for the description of the spatial structure of mitotic chromosomes. Despite…
Existing beam contact formulations can be categorized in point contact models that consider a discrete contact force at the closest point of the beams, and line contact models that assume distributed contact forces. In this work, it will be…
We demonstrate insights into the three-dimensional structure of defects in graphene, in particular grain boundaries, obtained via a new approach from two transmission electron microscopy images recorded at different angles. The structure is…
Chromatin fibers composed of DNA and proteins fold into consecutive loops to form rod-shaped chromosome in mitosis. Although the loop growth dynamics is investigated in several studies, its detailed processes are unclear. Here, we describe…
We developed a graph-based block-diagonalization (GBBD) method for the full configuration interaction Hamiltonian of molecular systems to efficiently calculate the exact eigenvalues of low-energy states. In this approach, the non-zero…
A living cell is an active environment where the organization and dynamics of chromatin are affected by different forms of activity. Optical experiments report that loci show subdiffusive dynamics and the chromatin fiber is seen to be…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
We present a theoretical analysis of the structural and mechanical properties of the 30-nm chromatin fiber. Our study is based on the two-angle model introduced by Woodcock et al. (Woodcock, C. L., S. A. Grigoryev, R. A. Horowitz, and N.…
This paper presents a novel approach using sensitivity analysis for generalizing Differential Dynamic Programming (DDP) to systems characterized by implicit dynamics, such as those modelled via inverse dynamics and variational or implicit…
We present an efficient algorithm to recover the three dimensional structure of a protein from its contact map representation. First we show that when a physically realizable map is used as target, our method generates a structure whose…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
We investigate the dynamics of two-photon correlations generated by the interaction of a three-level atom in the $\Xi$, $\Lambda$ or V configuration, with two classical external driving fields, under the rotating-wave approximation, in the…
Contact dynamics (CD) is a powerful method to solve the dynamics of large systems of colliding rigid bodies. CD can be computationally more efficient than classical penalty-based discrete element methods (DEM) for simulating contact between…
Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple…