Related papers: Phase Transition in Reconstituted Chromatin
We consider the large-time dynamics of one-dimensional processes involving adsorption and desorption of extended hard-core particles (dimers, trimers,\,$\cdots,k$-mers), while interacting through their constituent monomers. Desorption can…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
RSC is an essential chromatin remodeling factor that is required for the control of several processes including transcription, repair and replication. The ability of RSC to relocate centrally positioned mononucleosomes at the end of…
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
We explore the possibility for the reconstruction of the generative physical models describing interactions between atomic units in solids from observational electron microscopy data. Here, scanning transmission electron microscopy (STEM)…
Accurate computational ptychographic phase reconstructions are enabled by fast direct-electron cameras with high dynamic ranges used for four-dimensional scanning transmission electron microscopy (4D-STEM). The availability of open software…
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…
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active…
Phase-change memory (PCM), a promising candidate for next-generation non-volatile memories, exploits quenched glassy and thermodynamically stable crystalline states as reversibly switchable state variables. We demonstrate PCM functions…
Liquid-liquid phase separation plays a major role in the formation and maintenance of various membrane-less subcellular structures in the cytoplasm and nucleus of cells. Biological condensates contain enhanced concentrations of proteins and…
Kinetics of sequential first-order reactions occurring in a chromatographic medium is developed. A model for motion of substances of a chain 1 -> 2 -> 3 -> in an infinite chromatographic column is worked out, and a mathematical procedure…
We develop a model in the framework of nuclear fragmentation at thermodynamic equilibrium which can be mapped onto an Ising model with constant magnetization. We work out the thermodynamic properties of the model as well as the properties…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
In the high density low temperature limit, Quantum Chromodynamics (QCD) exhibits a transition to a phase characterized by color superconductivity and by energy gaps in the fermion spectra. Under specific circumstances the gap parameter has…
We study a random matrix model for the statistical properties of the purity of a bipartite quantum system at a finite (fictitious) temperature. This enables us to write the generating function for the cumulants, for both balanced and…
Materials with nanoscale phase separation are considered. A system representing a heterophase mixture of ferromagnetic and paramagnetic phases is studied. After averaging over phase configurations, a renormalized Hamiltonian is derived…
We consider a model of free fermions in a ladder geometry coupled to a nonuniform cavity mode via Peierls substitution. Since the cavity mode generates a magnetic field, no-go theorems on spontaneous photon condensation do not apply, and we…
Mixed-order phase transitions display a discontinuity in the order parameter like first-order transitions yet feature critical behavior like second-order transitions. Such transitions have been predicted for a broad range of equilibrium and…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…