Related papers: Chromatin state switching in a polymer model with …
Understanding coupled electron-phonon systems is one of the fundamental issues in strongly correlated systems. In this work, we aim to extend the notion of mixed-state phases to the realm of coupled electron/spinphonon systems.…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
We study first- and second-order phase transitions of ferromagnetic lattice models on scale-free networks, with a degree exponent $\gamma$. Using the example of the $q$-state Potts model we derive a general self-consistency relation within…
We investigate in this paper the ground state and the nature of the transition from an orientational ordered phase at low temperature to the disordered state at high temperature in a molecular crystal. Our model is a Potts model which takes…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
Mixed order phase transitions (MOT), which display discontinuous order parameter and diverging correlation length, appear in several seemingly unrelated settings ranging from equilibrium models with long-range interactions to models far…
Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relates to epigenetic state, remains unclear. We develop a theory…
We study dynamic behavior of Potts model with invisible states near the first-order phase transition temperature. We focus on melting process starting from the perfect ordered state. This model is regarded as a standard model to analyze…
We study phase transition behavior of the Heisenberg model on a distorted triangular lattice with competing interactions. The ground-state phase diagram indicates that underlying symmetry can be changed by tuning parameters. We focus on two…
A hybrid Potts model where a random concentration $p$ of the spins assume $q_0$ states and a random concentration $1-p$ of the spins assume $q>q_0$ states is introduced. It is known that when the system is homogeneous, with an integer spin…
We present a simple yet generic model for the behavior of a system of many surface-attached flexible polymers with rigid side chains. Beyond its potential application in describing the dynamics of the extracellular matrix of mammalian…
In spin crossover materials, an abrupt phase transition between a low spin state and a high spin state can be driven by temperature, pressure or by light irradiation. Of a special relevance are Fe(II) based coordination polymers where, in…
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…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
A two-state model Hamiltonian is proposed to model the coupling of twisting displacements to charge-transfer behavior in the ground and excited states of a general monomethine dye molecule. This coupling may be relevant to the molecular…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
We study the dynamical properties of the Mermin model, a simple quantum dissipative model with a monochromatic environment, using analytical and numerical methods. Our numerical results show that the model exhibits a second order phase…
This is an analytic study of the problem of transitions between normal and superconducting phases for a sample which encloses a magnetic flux. A preliminary study of this problem, based on numerical minimization of the free energy for a…
We present the results of a quantitative study of the phase behavior of a model polymer chain with side spheres using two independent computer simulation techniques. We find that the mere addition of side spheres results in key…