Related papers: Efficient simulation of semiflexible polymers
The scaling behaviour of randomly branched polymers in a good solvent is studied in two to nine dimensions, using as microscopic models lattice animals and lattice trees on simple hypercubic lattices. As a stochastic sampling method we use…
We present a comparative study of two computer simulation methods to obtain static and dynamic properties of dilute polymer solutions. The first approach is a recently established hybrid algorithm based upon dissipative coupling between…
The aim of this paper is to compare results from lattice-Boltzmann and Brownian dynamics simulations of linear chain molecules. We have systematically varied the parameters that may affect the accuracy of the lattice-Boltzmann simulations,…
Dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase…
We present a Generalized Langevin Equation for the dynamics of interacting semiflexible polymer chains, undergoing slow cooperative dynamics. The calculated Gaussian intermolecular center-of-mass and monomer potentials, wich enter the GLE,…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Transport of tracer particles through mesh-like environments such as biological hydrogels and polymer matrices is ubiquitous in nature. These tracers could be passive, such as colloids or active (self-propelled), such as synthetic…
Building on the results of our computer simulation (ArXiv cond-mat/0503573)we develop a theoretical description of the motion of a bead, embedded in a network of semiflexible polymers, and responding to an applied force. The theory reveals…
Analyzing the physical and chemical properties of single DNA based molecular machines such as polymerases and helicases often necessitates to track stepping motion on the length scale of base pairs. Although high resolution instruments have…
Standard algorithms for the numerical integration of the Langevin equation require that interactions are slowly varying during to the integration timestep. This in not the case for hard-body systems, where there is no clearcut between the…
A double-distribution-function based lattice Boltzmann method (DDF-LBM) is proposed for the simulation of polyatomic gases in the supersonic regime. The model relies on an extended equilibrium state that is constructed to reproduce the…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Langevin dynamics (LD) has been proven to be a powerful technique for optimizing a non-convex objective as an efficient algorithm to find local minima while eventually visiting a global minimum on longer time-scales. LD is based on the…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
We present here the systematic development of quantitative lattice simulations of dense polymers through a novel computational technique that allows for an efficient accounting of the chain conformations. Our approach is based on the…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Current dynamic networks and dynamic pruning methods have shown their promising capability in reducing theoretical computation complexity. However, dynamic sparse patterns on convolutional filters fail to achieve actual acceleration in…
We analyze the conformational dynamics and statistical properties of an active polymer model. The polymer is described as a freely-jointed bead-rod chain subject to stochastic active force dipoles that act on the suspending solvent where…