Related papers: Constraints, Histones, and the 30 Nanometer Spiral
A crystal lattice, when confined to the surface of a cylinder, must have a periodic structure that is commensurate with the cylinder circumference. This constraint can frustrate the system, leading to oblique crystal lattices or to…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
Experiments on the formation of spiraling hexagons (350 - 1000 nm in width) from a solution of nanoparticles are presented. Transmission electron microscopy images of the reaction products of chemically synthesized cadmium nanocrystals…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
We investigate the mechanisms of histone sliding and detachment with a stochastic model that couples thermally-induced, passive histone sliding with active motor-driven histone unwrapping. Analysis of a passive loop or twist defect-mediated…
Elucidating the interplay of stress and geometry is a fundamental scientific question arising in multiple fields. In this work, we investigate the geometric frustration of crystalline caps confined on the sphere in both elastic and plastic…
We generalize the shape optimization problem for the existence of stable equilibrium configurations of nematic and cholesteric liquid crystal drops surrounded by an isotropic solution to include a broader family of admissible domains with…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
The spin of an electron or a nucleus in a semiconductor [1] naturally implements the unit of quantum information -- the qubit -- while providing a technological link to the established electronics industry [2]. The solid-state environment,…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…