Related papers: Statistical physics of the melting of inhomogeneou…
We explore the melting of a lattice DNA in the presence of atmospheric disorder, which mimics the crowded environment inside the cell nucleus, using Monte Carlo simulations. The disorder is modeled by randomly retaining lattice sites with…
In [arXiv:1806.06668], we have studied the Boltzmann random triangulation of the disk coupled to an Ising model on its faces with Dobrushin boundary condition at its critical temperature. In this paper, we investigate the phase transition…
A non-isothermal phase field model that captures both displacive and diffusive phase transformations in a unified framework is presented. The model is developed in a formal thermodynamic setting, which provides guidance on admissible…
In the framework of the theoretical model of the phase transition of binary solutions into spatially inhomogeneous states proposed earlier by the autors [1], which takes into account nonlinear effects, the role of the cubic in concentration…
The influence of the atomic-scale inhomogeneities of the pairing interaction on the superconducting order parameter distribution and the LDOS is studied in the framework of mean-field BCS theory for two-dimensional lattice model. It is…
We define a DNA as a sequence of $\pm 1$'s and embed it on a path of Cayley tree. Using group representation of the Cayley tree, we give a hierarchy of a countable set of DNAs each of which 'lives' on the same Cayley tree. This hierarchy…
These notes are devoted to the statistical mechanics of directed polymers interacting with one-dimensional spatial defects. We are interested in particular in the situation where frozen disorder is present. These polymer models undergo a…
The thermodynamics of the $q$-state Potts model with arbitrary $q$ on a class of hierarchical lattices is considered. Contrary to the case of the crystal lattices, it has always the second-order phase transitions. The analytical expressions…
In low temperature supercooled liquid, below the ideal mode coupling theory transition temperature, hopping and continuous diffusion are seen to coexist. We present a theory which incorporates interaction between the two processes and shows…
We present results of large-scale Monte Carlo simulations for a three-dimensional Ising model with short range interactions and planar defects, i.e., disorder perfectly correlated in two dimensions. We show that the phase transition in this…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
We study the effect of crowders on the melting profile of homogeneous and heterogeneous DNA molecules. We find out the melting profile of short DNA molecules and compare our findings with the experiments. We consider some random…
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…
Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length $\xi_c$. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA…
We use computer simulations to study the microscopic dynamics of an athermal assembly of soft particles near the fluid-to-solid, jamming transition. Borrowing tools developed to study dynamic heterogeneity near glass transitions, we…
This work studies the effect of the heterogeneity of a porous medium on convective mixing. We consider a system where a Rayleigh-B\'enard instability is triggered by a temperature difference between the top and bottom boundaries.…
Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is…
The dissipative nature of heat transfer relaxes thermal flows to an equilibrium state that is devoid of temperature gradients. The distance to reach an equilibrium temperature -- the thermal entrance length -- is a consequence of diffusion…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…