Hydrodynamic screening near planar boundaries: effects on semiflexible polymer dynamics

The influence of hydrodynamic screening near a surface on the dynamics of a single semiflexible polymer is studied by means of Brownian dynamics simulations and hydrodynamic mean field theory. The polymer motion is characterized in terms of the mean squared displacements of the end-monomers, the end-to-end vector, and the scalar end-to-end distance. In order to control hydrodynamic screening effects, the polymer is confined to a plane at a fixed separation from the wall. When gradually decreasing this separation, a crossover from Zimm-type towards Rouse (free-draining) polymer dynamics is induced. However, this crossover is rather slow and the free-draining limit is not completely reached--substantial deviations from Rouse-like dynamics are registered in both simulations and theory--even at distances of the polymer from the wall on the order of the monomer size. Remarkably, the effect of surface-induced screening of hydrodynamic interactions sensitively depends on the type of dynamic observable considered. For vectorial quantities such as the end-to-end vector, hydrodynamic interactions are important and therefore surface screening effects are sizeable. For a scalar quantity such as the end-to-end distance, on the other hand, hydrodynamic interactions are less important, but a pronounced dependence of dynamic scaling exponents on the persistence length to contour length ratio becomes noticeable. Our findings are discussed against the background of single-molecule experiments on f-actin [L. Le Goff et al., Phys. Rev. Lett. 89, 258101 (2002)].     

Secondary structure formation of homopolymeric single-stranded nucleic acids including force and loop entropy: Implications for DNA hybridization

Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy —c ln m for a loop of length m, we study homopolymeric single-stranded nucleic acid chains under external force and varying temperature. In the thermodynamic limit of a long strand, the chain displays a phase transition between a low-temperature/low-force compact (folded) structure and a high-temperature/high-force molten (unfolded) structure. The influence of c on phase diagrams, critical exponents, melting, and force extension curves is derived analytically. For vanishing pulling force, only for the limited range of loop exponents 2 < c ≲ 2.479 a melting transition is possible; for c ≤ 2 the chain is always in the folded phase and for 2.479 ≲ c always in the unfolded phase. A force-induced melting transition with singular behavior is possible for all loop exponents c < 2.479 and can be observed experimentally by single-molecule force spectroscopy. These findings have implications for the hybridization or denaturation of double-stranded nucleic acids. The Poland-Scheraga model for nucleic acid duplex melting does not allow base pairing between nucleotides on the same strand in denatured regions of the double strand. If the sequence allows these intra-strand base pairs, we show that for a realistic loop exponent c ≈ 2.1 pronounced secondary structures appear inside the single strands. This leads to a lower melting temperature of the duplex than predicted by the Poland-Scheraga model. Further, these secondary structures renormalize the effective loop exponent [^(c)] \hat{{c}}, which characterizes the weight of a denatured region of the double strand, and thus affect universal aspects of the duplex melting transition.     

Single flexible and semiflexible polymers at high shear: Non-monotonic and non-universal stretching response

Using Brownian hydrodynamic simulation techniques, we study single polymers in shear. We investigate the effects of hydrodynamic interactions, excluded volume, chain extensibility, chain length and semiflexibility. The well-known stretching behavior with increasing shear rate [(g)\dot] \dot{{\gamma}} is only observed for low shear [(g)\dot] \dot{{\gamma}} < [(g)\dot]^max \dot{{\gamma}}^{{\max}}_{} , where [(g)\dot]^max \dot{{\gamma}}^{{\max}}_{} is the shear rate at maximum polymer extension. For intermediate shear rates [(g)\dot]^max \dot{{\gamma}}^{{\max}}_{} < [(g)\dot] \dot{{\gamma}} < [(g)\dot]^min \dot{{\gamma}}^{{\min}}_{} the radius of gyration decreases with increasing shear with minimum chain extension at [(g)\dot]^min \dot{{\gamma}}^{{\min}}_{} . For even higher shear [(g)\dot]^min \dot{{\gamma}}^{{\min}}_{} < [(g)\dot] \dot{{\gamma}} the chain exhibits again shear stretching. This non-monotonic stretching behavior is obtained in the presence of excluded-volume and hydrodynamic interactions for sufficiently long and inextensible flexible polymers, while it is completely absent for Gaussian extensible chains. We establish the heuristic scaling laws [(g)\dot]^max \dot{{\gamma}}^{{\max}}_{} ∼ N ^-1.4 and [(g)\dot]^min \dot{{\gamma}}^{{\min}}_{} ∼ N ^0.7 as a function of chain length N , which implies that the regime of shear-induced chain compression widens with increasing chain length. These scaling laws also imply that the chain response at high shear rates is not a universal function of the Weissenberg number Wi = [(g)\dot] \dot{{\gamma}} t \tau anymore, where t \tau is the equilibrium relaxation time. For semiflexible polymers a similar non-monotonic stretching response is obtained. By extrapolating the simulation results to lengths corresponding to experimentally studied DNA molecules, we find that the shear rate [(g)\dot]^max \dot{{\gamma}}^{{\max}}_{} to reach the compression regime is experimentally realizable.     

EFFECT OF COMPOSITION AND PROCESSING CONDITION ON MICROSTRUCTURAL PROPERTIES AND DURABILITY OF FLUOROPOLYMER/ACRYLIC BLENDS

Fluoropolymer blends have been widely used as binders for exterior coatings because of their excellent resistance to ultra-violet (UV) radiation as well as to many corrosive chemical agents.It is known that the fluorinated component usually has a lower glass transition temperature and easily crystallizes in the final structure depending upon the blend composition and sample annealing condition.We investigated the effect of blend composition and annealing process (slow and fast cooling) on the surface mor...     

High-Order Time Integration in the p-Version of Finite Elements

In isothermal solid mechanics, the space and time domain need to be discretized. This paper presents an approach using high-order finite elements based on Legendre polynomials for the spatial discretization and time-adaptive diagonal-implicit Runge-Kutta methods for the temporal discretization. The superiority of this approach over a traditional one using linear shape functions for the space domain and a Backward-Euler scheme for the time domain is demonstrated. (© 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Diastereoselective propargylations with planar chiral chromiumcarbonyl arene complex substituted propargyl cations

The ionization of planar chiral ortho-substituted (arene)Cr(CO)(3)-substituted alpha-propargylic acetates 3 with Lewis acids results in the formation of stable (arene)Cr(CO)(3)-substituted alpha-propargyl cations 4. Subsequent additions of sulfur, nitrogen, oxygen, and pi-carbon nucleophiles to these organometallic electrophiles give rise to the regio- and highly diastereoselective formation of propargyl derivatives 5 in good yields (44-90%; dr = 70:30 to >99:1). The relative stereochemistry of the propargyl acetates 3 and the trapping products 5 was established by several crystal structure analyses, indicating that the cationic propargylations occurred under retention of configuration at the propargylic center. Most important for the diastereoselectivity of the nucleophilic trapping reaction is the configurational stability of the diastereotopic cation 4 as reflected by substituent effects. In situ ionizations according to an S(N)1-mechanism not only result in a considerable loss but also in an inversion of diastereoselectivity.     

Decoherence via the dynamical casimir effect

We derive a master equation for a mirror interacting with the vacuum field via radiation pressure. The dynamical Casimir effect leads to decoherence of a superposition state in a time scale that depends on the degree of "macroscopicity" of the state components, and which may be much shorter than the relaxation time scale. Coherent states are selected by the interaction as pointer states.     

Electromagnetically induced quantum memory

We discuss the problem of creating coherence in an optically driven quantum system in conditions where decoherence is caused by the laser field itself, due to coupling of the system to a rapidly decaying state or continuum. It is shown that by applying an additional laser field between this state and a bound state the relaxation channel can be suppressed as a result of a "dark state" formation, giving rise to long living Rabi oscillations in the system. It is found that the same mechanism of preserving coherence exists in systems with level splitting or degeneracy, where the driving field interacts with multiple resonant sublevels simultaneously. We also show that specific coherent propagation phenomena assisted by the interference suppression of decoherence can be observed under these conditions.     

Salt-induced DNA-histone complexation

We study numerically the binding of one semiflexible charged polymer onto an oppositely charged sphere. Using parameters appropriate for DNA-histone complexes, we find complete wrapping for intermediate salt concentrations only, in agreement with experiments. For high salt concentrations, a strongly discontinuous dewrapping occurs. For low salt concentrations, we find multiple conformational transitions, leading to an extended DNA configuration. The wrapped states are characterized by spontaneously broken rotational and mirror symmetries, giving rise to four distinct structures.