Related papers: Randomly cross-linked polymer models
We consider polymers in which M randomly selected pairs of monomers are restricted to be in contact. Analytical arguments and numerical simulations show that an ideal (Gaussian) chain of N monomers remains expanded as long as M<<N. This…
Modeling of polymer chains has received a lot of attention in mathematics. In fact, probabilistic models that naturally arise in statistical mechanics have been widely studied by mathematicians for the very challenging and novel problems…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
We present simulations on a binary blend of bead-spring polymer chains. The introduction of monomer size disparity yields very different relaxation times for each component of the blend. Competition between two different arrest mechanisms,…
We present molecular dynamics simulations on the structural relaxation of a simple bead-spring model for polymer blends. The introduction of a different monomer size induces a large time scale separation for the dynamics of the two…
The some dynamic properties of a random heteropolymer in the condensed state are studied in the mode coupling approximation. In agreement with recent report a dynamic friction increasing is predicted for the random heteropolymer with…
We propose a new toy model of a heteropolymer chain capable of forming planar secondary structures typical for RNA molecules. In this model the sequential intervals between neighboring monomers along a chain are considered as quenched…
The conformations of interacting linear polymers on a dynamical planar random lattice are studied using a random two-matrix model. An exact expression for the partition function of self-avoiding chains subject to attractive contact…
We use lattice-Boltzmann molecular dynamics (LBMD) simulations to study the compression of a confined polymer immersed in a fluid and pushed by a large spherical colloid with a diameter comparable to the channel width. We examined the…
We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by…
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…
Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
We address the physics of nematic liquid crystalline elastomers randomly crosslinked in the isotropic state. To do this, we construct a phenomenological effective replica Hamiltonian in terms of two order-parameter fields: one for the…
Linear mixed models (LMMs) are used as an important tool in the data analysis of repeated measures and longitudinal studies. The most common form of LMMs utilize a normal distribution to model the random effects. Such assumptions can often…
Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The…
We model the behaviour of a single colloid embedded in a cross-linked polymer gel, immersed in a viscous background fluid. External fields actuate the particle into a periodic motion, which deforms the embedding matrix and creates a local…
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…