Related papers: A Self Healing Model Based on Polymer-Mediated Chr…
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 large-scale molecular dynamics simulations for a coarse-grained model of polymer melts in equilibrium. From detailed Rouse mode analysis we show that the time-dependent relaxation of the autocorrelation function (ACF) of modes…
We consider a generalization of the discrete-time Self Healing Umbrella Sampling method, which is an adaptive importance technique useful to sample multimodal target distributions. The importance function is based on the weights (namely the…
We study pore nucleation in a model membrane system, a freestanding polymer film. Nucleated pores smaller than a critical size close, while pores larger than the critical size grow. Holes of varying size were purposefully prepared in liquid…
Complexation of polymers at liquid interfaces is an emerging technique to produce all-liquid printable and self-healing devices and membranes. It is crucial to control the assembly process but the mechanisms at play remain unclear. Using…
In a recent publication [Phys. Rev. Lett. 97, 227402 (2006), cond-mat/0611411], it has been demonstrated numerically that a long-range disorder potential in semiconductor quantum wells can be reconstructed reliably via single-photon…
The long-time dynamics of the 1D contact process suddenly brought out of an uncorrelated initial state is studied through a light-cone transfer-matrix renormalisation group approach. At criticality, the system undergoes ageing which is…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
In reconstituting k-mer models, extended objects which occupy several sites on a one dimensional lattice, undergo directed or undirected diffusion, and reconstitute -when in contact- by transferring a single monomer unit from one k-mer to…
The method of angular photonic correlations of spontaneous emission is introduced as an experimental, purely optical scheme to characterize disorder in semiconductor nanostructures. The theoretical expression for the angular correlations is…
We model the effect of pump depletion on reversible photodegradation using the extended domain model[Anderson and Kuzyk, arXiv:1309.5176v1, 2013] and the Beer-Lambert law. We find that neglecting pump absorption in the analysis of the…
We study the density-density correlation function of the dense random heteropolymer solutions. We show that a phase transition is possible due to the heterogeneity of polymers. We also show that the critical behavior of the system is…
The specific heat is a central property of condensed matter systems including polymers and oligomers in their condensed phases. Yet, predictions of this quantity from molecular simulations and successful comparisons to experimental data are…
The random-dimer model is probably the most popular model for a one-dimensional disordered system where correlations are responsible for delocalization of the wave functions. This is the primary model used to justify the insulator-metal…
The effect of confinement in the segmental relaxation of polymers is considered. On the basis of a thermodynamic model we discuss the emerging relevance of the fast degrees of freedom in stimulating the much slower segmental relaxation, as…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
Behavior of two-time autocorrelation during the phase separation in solid binary mixtures are studied via numerical solutions of the Cahn-Hilliard equation as well as Monte Carlo simulations of the Ising model. Results are analyzed via…
The transport coefficients of dense polymeric fluids are approximately calculated from the microscopic intermolecular forces. The following finite molecular weight effects are discussed within the Polymer-Mode-Coupling theory (PMC) and…
A method is presented that, when used in conjunction with single molecule experimental techniques, allows for the extraction of rates and mechanical properties of a biomolecule undergoing transitions between mechanically distinct states.…
A self-consistent mode-coupling theory is presented for the viscosity of solutions of charged rod-like polymers. The static structure factor used in the theory is obtained from polymer integral equation theory; the Debye-H\"{u}ckel…