For the interpretation of solution structural and dynamic data of linear and circular DNA molecules in the kb range, and for the prediction of the effect of local structural changes on the global conformation of such DNAs, we have developed an efficient and easy way to set up a program based on a second-order explicit Brownian dynamics algorithm. The DNA is modeled by a chain of rigid segments interacting through harmonic spring potentials for bending, torsion, and stretching. The electrostatics are handled using precalculated energy tables for the interactions between DNA segments as a function of relative orientation and distance. Hydrodynamic interactions are treated using the Rotne-Prager tensor. While maintaining acceptable precision, the simulation can be accelerated by recalculating this tensor only once in a certain number of steps.

Collisions of Au on Au at incident energies of 150, 250 and 400 A MeV were studied with the FOPI-facility at GSI Darmstadt. Nuclear charge (Z ≤ 15) and velocity of the products were detected with full azimuthal acceptance at laboratory angles 1 • ≤ θ lab ≤ 30 • . Isotope separated light charged particles were measured with movable multiple telescopes in an angular range of 6 − 90 • . Central collisions representing about 1% of the reaction cross section were selected by requiring high total transverse energy, but vanishing sideflow. The velocity space distributions and yields of the emitted fragments are reported. The data are analysed in terms of a thermal model including radial flow. A comparison with predictions of the Quantum Molecular Model is presented.PACS: 25.70.Pq

We study static and dynamic properties of polymer brushes of moderate and high grafting densities using molecular dynamics simulations. The self-consistent-field theory is able to reproduce the observed density profiles once finite extensibility of the chains is included. A similar approach, using a Langevin-type model to account for a coupling between the vertical and lateral chain fluctuations, is successfully implemented to explain the lateral chain fluctuations at moderate-to-high grafting densities. The corresponding fluctuation dynamics in the direction lateral to the surface is well described by Rouse scaling. The dependence of the dynamics on grafting density (concentration) is very well described by the dynamic behavior of thermal blobs for the fluctuations in the direction both perpendicular and parallel to the surface. We find an anisotropic fluctuation dynamics related with two characteristic dynamic length scales in the both directions. We have further investigated the pulling forces acting on the polymer bonds. The force acting on the first bond directly connected to the surface is reduced at higher grafting densities, which is explained with an entropic contribution to the bond tension. A nonvanishing end-monomer tension is observed at high grafting densities. The integrated force (excess free energy) follows the prediction of the thermal blob model of the brush.

Mixed polymer brushes as functional ultra thin films for surface functionalization have an enormous potential to create a variety of smart, switchable, and multifunctional surfaces and thin films. It is shown how computer simulations can contribute to a better understanding of the switching behavior of brushes. Furthermore, it is described how polymer brushes can be used to create surfaces with switchable ultrahydrophobicity and wettability gradients, as well as functional layers for the immobilization of nanoparticles. Applications of these versatile and multifunctional brush coatings are envisioned in many areas including fluid control, microfluidics, and thin film sensors.

The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is verified by numerical simulations. The results confirm that the unspecific binding of protein to DNA, combined with sliding, is capable to reduce the reaction times significantly.

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A Brownian dynamics (BD) model described in the accompanying paper (Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA, and other wormlike chain polyelectrolytes. Biophys. J. 74:000-000) has been used for computing the end-to-end distance distribution function, the cyclization probability, and the cyclization kinetics of linear DNA fragments between 120 and 470 basepairs with optional insertion of DNA bends. Protein-mediated DNA loop formation was modeled by varying the reaction distance for cyclization between 0 and 10 nm. The low cyclization probability of DNA fragments shorter than the Kuhn length (300 bp) is enhanced by several orders of magnitude when the cyclization is mediated by a protein bridge of 10 nm diameter, and/or when the DNA is bent. From the BD trajectories, end-to-end collision frequencies were computed. Typical rates for loop formation of linear DNAs are 1.3 x 10(3) s(-1) (235 bp) and 4.8 x 10(2) s(-1) (470 bp), while the insertion of a 120 degree bend in the center increases this rate to 3.0 x 10(4) s(-1) (235 bp) and 5.5 x 10(3) s(-1) (470 bp), respectively. The duration of each encounter is between 0.05 and 0.5 micros for these DNAs. The results are discussed in the context of the interaction of transcription activator proteins.

Via computer simulations, we demonstrate how a densely grafted layer of polymers, a brush, could be turned into an efficient switch through chemical modification of some of its end monomers. In this way, a surface coating with reversibly switchable properties can be constructed. We analyze the fundamental physical principle behind its function, a recently discovered surface instability, and demonstrate that the combination of a high grafting density, an inflated end-group size, and a high degree of monodispersity is a condition for an optimal functionality of the switch.