Related papers: Effective equations for reaction coordinates in po…
We perform, with the help of cloud computing resources, extensive Langevin simulations which provide compelling evidence in favor of a general markovian framework for unbiased polymer translocation. Our statistical analysis consists of…
The influence of monomer-monomer interactions on the scaling exponents and shape characteristics of a single polymer chain in a selective solvent is investigated using Langevin dynamics simulations. By systematically increasing the…
We present a unified theory for the longitudinal dynamic response of a stiff polymer in solution to various external perturbations (mechanical excitations, hydrodynamic flows, electrical fields, temperature quenches ...) that can be…
We use Newtonian and overdamped Langevin dynamics to study long flexible polymers dragged by an external force at a constant velocity $v$. The work $W$ by that force depends on the initial state of the polymer and the details of the…
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…
We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…
Since Kramers' pioneering work in 1940, significant efforts have been devoted to studying Langevin equations applied to physical and chemical reactions projected onto few collective variables, with particular focus on the inference of their…
The local dynamical features of a PEO melt studied by MD simulations are compared to two model chain systems, namely the well-known Rouse model as well as the semiflexible chain model (SFCM) that additionally incorporates chain stiffness.…
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…
Complex Langevin dynamics can be used to perform numerical simulations of theories with a complex action. In order to justify the procedure, it is important to understand the properties of the real and positive distribution, which is…
Solutions of interacting linear polymers are mapped onto a system of ``soft'' spherical particles interacting via an effective pair potential. This coarse-graining reduces the individual monomer-level description to a problem involving only…
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 out-of-equilibrium large time dynamics of a gaussian polymer chain in a quenched random potential. The dynamics studied is a simple Langevin dynamics commonly referred to as the Rouse model. The equations for the two-time…
The relaxation dynamics of a polymer wound around a fixed obstacle constitutes a fundamental instance of polymer with twist and torque and it is of relevance also for DNA denaturation dynamics. We investigate it by simulations and Langevin…
The recently discovered supersymmetric generalizations of Langevin dynamics and Kramers equation can be utilized for the exploration of free energy landscapes of systems whose large time-scale separation hampers the usefulness of standard…
The longitudinal response of single semiflexible polymers to sudden changes in externally applied forces is known to be controlled by the propagation and relaxation of backbone tension. Under many experimental circumstances, realized, e.g.,…
Based on a Hamiltonian that incorporates the elastic coupling between a tracer and active particles, we derive a generalized Langevin model for the non-equilibrium mechanical response of active viscoelastic biomatter. Our model accounts for…
One important problem in constructing the reduced dynamics of molecular systems is the accurate modeling of the non-Markovian behavior arising from the dynamics of unresolved variables. The main complication emerges from the lack of scale…