Related papers: Phase Transition in Reconstituted Chromatin
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…
A recent letter [Lin & Goldman, Phys. Rev. Lett. 106, 127003 (2011)] has presented experimental data in highly disordered thin films, which were interpreted as a quantum phase transition, an intriguing and surprising result for this system.…
Electron tomography is a technique used in both materials science and structural biology to image features well below optical resolution limit. In this work, we present a new algorithm for reconstructing the three-dimensional(3D)…
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 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.…
Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…
We use the density functional method to examine the properties of the nonuniform (two-phase) fluid of two-level atoms, a part of which is excited. Basing on the analysis of the equation of state of a gas of two-level atoms, a part of which…
At high temperatures or densities, hadronic matter shows different forms of critical behaviour: colour deconfinement, chiral symmetry restoration, and diquark condensation. I first discuss the conceptual basis of these phenomena and then…
We present a numerical technique employing the density of partition function zeroes (i) to distinguish between phase transitions of first and higher order, (ii) to examine the crossover between such phase transitions and (iii) to measure…
This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths,…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
The evolution of the atomic structures of the combinatorial library of Sm-substituted thin film BiFeO3 along the phase transition boundary from the ferroelectric rhombohedral phase to the non-ferroelectric orthorhombic phase is explored…
Atomically thin 2-dimensional heterostructures are a promising, novel class of materials with groundbreaking properties. The possiblity of choosing the many constituent components and their proportions allows optimizing these materials to…
The folding and structure of biomacromolecules depend on the 3D distributions of their constituents, which ultimately controls their functionalities and interactions with other biomacromolecules. Atom probe tomography (APT) with its…