Related papers: Randomly cross-linked polymer models
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
We study percolation and the random cluster model on the triangular lattice with 3-body interactions. Starting with percolation, we generalize the star--triangle transformation: We introduce a new parameter (the 3-body term) and identify…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
Much work has studied effective interactions between micron-sized particles carrying linkers forming reversible, inter-particle linkages. These studies allowed understanding the equilibrium properties of colloids interacting through…
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…
Machine learning (ML) is rapidly transforming the way molecular dynamics simulations are performed and analyzed, from materials modeling to studies of protein folding and function. ML algorithms are often employed to learn low-dimensional…
We study two cross-linked polymer systems in the strong stretching regime. The first consists of two polymers sharing one endpoint, with the other two endpoints coupled by a harmonic potential. Within the weakly bending approximation, we…
A generalized vertex join of a graph is obtained by joining an arbitrary multiset of its vertices to a new vertex. We present a low-order polynomial time algorithm for finding the chromatic polynomials of generalized vertex joins of trees,…
To identify an analytical relation between the properties of polymers and their's monomer a Metal-Molecule-Metal (MMM) junction has been presented as an interesting and widely used object of research in which the molecule is a polymer which…
Active loop extrusion - the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes - is firmly established mechanism responsible for chromatin spatial organization at different…
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…
Heterogeneous distribution of passive and active domains in the chromosome plays a crucial role for its dynamic organization within the cell nucleus. Motivated by that here we investigate the steady-state conformation and dynamics of a…
In this article, we try to give a rather complete picture of the behavior of the free energy for a model of directed polymer in a random environment, in which the polymer is a simple symmetric random walk on the lattice $\Z^d$, and the…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
We have developed a theory of polymer entanglement using an extended Cahn-Hilliard functional, with two extra terms. One is a nonlocal attractive term, operating over mesoscales, which is interpreted as giving rise to entanglement, and the…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…