We have performed a multicanonical molecular dynamics simulation on a simple model protein. We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers. Since the hydrophobic interaction is considered to significantly affect protein folding, we particularly focus on the competition between effects of the Coulomb interaction and the hydrophobic interacti...

– Bead spring models for polymers in solution are nonlinear if either the finite extensibility of the polymer, excluded volume effects or hydrodynamic interactions between polymer segments are taken into account. For such models we use a powerful method for the determination of the complete relaxation spectrum of fluctuations at steady state. In general, the spectrum and modes differ significan...

We present a study of the coarse-graining of polymers into bead-spring chains using statistical mechanics. The force–extension behavior is examined at different levels of coarse-graining. A direct result of the springs being decoupled is that the force–extension behavior depends only on the number of flexibility lengths (e.g. persistence or Kuhn lengths) represented by each spring. This dimensi...

We investigate the dynamics and pathways of the collapse of a single, semiflexible polymer in a poor solvent via three-dimensional Brownian Dynamics simulations. An example of this phenomenon is DNA condensation induced by multivalent cations. Earlier work indicates that the collapse of semiflexible polymers generically proceeds via a cascade through metastable racquet-shaped, long-lived interm...

Linear viscoelastic properties for a dilute polymer solution are predicted by modeling the solution as a suspension of non-interacting bead-spring chains. The present model, unlike the Rouse model, can describe the solution’s rheological behavior even when the solvent quality is good, since excluded volume effects are explicitly taken into account through a narrow Gaussian repulsive potential b...

2014 The dynamical exponent z for a single polymer chain in a good solvent is obtained to order 03B5 (= 4 d) for the bead and spring (Rouse-Zimm) model. In the free-draining limit z = 4 03B5/4 + ..., a result in agreement with a phenomenological prediction that z = 2 + 1/03BD due to de Gennes. In the non-free draining limit, z = 4 5 03B5/4 + ..., which disagrees with de Gennes’ prediction that ...

We present a new closure for the mean rate of stretching of a dissolved polymer by homogeneous isotropic turbulence. The polymer is modeled by a bead-spring-type model (e.g., Oldroyd B, FENE-P, Giesekus) and the analytical closure is obtained assuming the Lagrangian velocity gradient can be modeled as a Gaussian, white-noise stochastic process. The resulting closure for the mean stretching depe...

DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In particular, the experimentally observed migration order of lambda - and T2-DNA molecules is reproduced by the simulations. The simulation data indicate that ...

Novel structural transitions of solvent-free oligomer-grafted nanoparticles are investigated by using molecular dynamics simulations of a coarse-grained bead-spring model. Variations in core size and grafting density lead to self-assembly of the nanoparticles into a variety of distinct structures. At the boundaries between different structures, the nanoparticle systems undergo thermoreversible ...