Linear and nonlinear photoexcitation dynamics in pi-conjugated polymers

Linear and nonlinear recombination kinetics with various lifetime distributions were identified for long-lived photoexcitations in a series of pi-conjugated polymer films using modulation frequency and excitation intensity dependencies of the photoinduced absorption. This includes monomolecular, bimolecular, and defect-limited recombination processes that lead to saturation. Using generalized kinetics parameters, we found characteristic plots for all recombination processes. Specifically, the bimolecular recombination process shows superlinear intensity dependence away from the steady state; on the contrary, dispersive bimolecular recombination leads to sublinear dependence.     

Relaxation dynamics of semiflexible polymers

We study the relaxation dynamics of a semiflexible chain by introducing a time-dependent tension. The chain has one of its ends attached to a large bead, and the other end is fixed. We focus on the initial relaxation of the chain that is initially strongly stretched. Using a tension that is self-consistently determined, we obtain the evolution of the end-to-end distance with no free parameters. Our results are in good agreement with single molecule experiments on double stranded DNA.     

Stretching dynamics of semiflexible polymers

We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the propagation speed of the backbone tension which is induced in response to stretching. Here, we employ a newly developed unified theory to systematically substantiate, restrict, and extend these approaches. Introducing the practically relevant scenario of a chain equilibrated under some prestretching force f _pre that is suddenly exposed to a different external force f _ext at the ends, we give a concise physical explanation of the underlying relaxation processes by means of an intuitive blob picture. We discuss the corresponding intermediate asymptotics, derive results for experimentally relevant observables, and support our conclusions by numerical solutions of the coarse-grained equations of motion for the tension.     

Molecular dynamics and strengthening of liquid-crystal polymers

The role of large-scale molecular motion in the self-organization and strengthening of liquid-crystal polymer fibers is discussed. It is shown that, at high temperatures, these objects are oriented liquid-crystal melts in which macromolecules remain extended but execute high-frequency conformational motions without leaving the tube approximately 20 Å in diameter. This large-scale motion is referred to as quasi-segmental motion. During annealing, the chains involved in quasi-segmental motion can accomplish longitudinal displacements (reptate) over considerable distances. It is this reptation that favors spontaneous self-organization and, consequently, strengthening of liquid-crystal polymer fibers upon heat treatment. The role played by the quasi-segmental motion of rigid macromolecules in the strengthening of polymers of different types is compared with the role played by the segmental motion of flexible chains in this process.     

Twist and writhe dynamics of stiff polymers

I consider the dynamics of a stiff filament, in particular the coupling of twist and bend via writhe. The time dependence of the writhe of a filament of length L is ([Wr(t) - Wr(0)]2) > approximately Lt(1/4). Simulations, on a simple model of a stiff polymer, are used to confirm scaling arguments. Fuller's theorem, and its relation with geometric phases, is reconsidered for open filaments.     

Pulling pinned polymers and unzipping DNA

We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA. When the pulling force is increased to a critical value, an "unzipping" transition occurs. For random DNA sequences with short-ranged correlations, we obtain exact results for the number of monomers liberated and the specific heat, including the critical behavior at the transition. Related systems include a random heteropolymer pulled away from an adsorbing surface and a vortex line in a type II superconductor tilted away from a fragmented columnar defect.     

Direct observation of multiple pathways of single-stranded DNA stretching

We observed multiple pathways of stretching single-stranded polydeoxynucleotides, poly(dA). Poly(dA) has been shown to undergo unique transitions under mechanical force, and such transitions were attributed to the stacking characteristics of poly(dA). Using single-molecule manipulation studies, we found that poly(dA) has two stretching pathways at high forces. The previously observed pathway has a free energy that is less than what is expected of single-stranded DNA with a random sequence, indicating the existence of a novel conformation of poly(dA) at large extensions. We also observed stepwise transitions between the two pathways by pulling the molecule with constant force, and found that the transitions are cooperative. These results suggest that the unique mechanical property of poly(dA) may play an important role in biological processes such as gene expression.     

Creeping friction dynamics and molecular dissipation mechanisms in glassy polymers

The dissipation mechanism of nanoscale kinetic friction between an atomic force microscopy tip and a surface of amorphous glassy polystyrene has been studied as a function of two parameters: the scanning velocity and the temperature. Superposition of the friction results using the method of reduced variables revealed the dissipative behavior as an activated relaxation process with a potential barrier height of 7.0 kcal/mol, corresponding to the hindered rotation of phenyl groups around the C-C bond with the backbone. The velocity relationship with friction F(v) was found to satisfy simple fluctuation surface potential models with F proportional to const-ln(v) and F proportional to const-ln(v)2/3.     

Loop dynamics in DNA denaturation

The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The long-time decay of the autocorrelation function is expressed in terms of the loop exponent c both for homopolymers and heteropolymers. This suggests an experimental method for measuring the exponent c using florescence correlation spectroscopy.     

Structure and switching of single-stranded DNA tethered to a charged nanoparticle surface

Using a molecular theory, we investigate the temperature-dependent self-assembly of single-stranded DNA(ss DNA)tethered to a charged nanoparticle surface. Here the size, conformations, and charge properties of ss DNA are taken into account. The main results are as follows: i) when the temperature is lower than the critical switching temperature, the ss DNA will collapse due to the existence of electrostatic interaction between ss DNA and charged nanoparticle surface; ii)for the short ss DNA chains with the number of bases less than 10, the switching of ss DNA cannot happen, and the critical temperature does not exist; iii) when the temperature increases, the electrostatic attractive interaction between ss DNA and charged nanoparticle surface becomes weak dramatically, and ss DNA chains will stretch if the electrostatic attractive interaction is insufficient to overcome the elastic energy of ss DNA and the electrostatic repulsion energy. These findings accord well with the experimental observations. It is predicted that the switching of ss DNA will not happen if the grafting densities are too high.     

Single molecule lifetime fluctuations reveal segmental dynamics in polymers

We present a single molecule fluorescence study that allows one to probe the nanoscale segmental dynamics in amorphous polymer matrices. By recording single molecular lifetime trajectories of embedded fluorophores, peculiar excursions towards longer lifetimes are observed. The asymmetric response is shown to reflect variations in the photonic mode density as a result of the local density fluctuations of the surrounding polymer. We determine the number of polymer segments involved in a local segmental rearrangement volume around the probe. A common decrease of the number of segments with temperature is found for both investigated polymers, poly(styrene) and poly(isobutylmethacrylate). Our novel approach will prove powerful for the understanding of the nanoscale rearrangements in functional polymers.     

Molecular dynamics study of tethered polymers in shear flow

Single macromolecules can now be isolated and characterized experimentally using techniques such as optical tweezers and videomicroscopy. An interesting and important single-molecule problem is that of the dynamics of a polymer chain tethered to a solid surface and subjected to a shear flow. An experimental study of such a system was reported by Doyle et al. (Phys. Rev. Lett. 84, 4769 (2000)), and their results showed a surprising recirculating motion of the DNA chain. We explore this problem using molecular dynamics computer simulations with explicit hydrodynamic interactions. The dynamical properties of a Freely Jointed Chain (FJC) with Finitely Extensible Nonlinear Elastic (FENE) links are examined in similar conditions (i.e., confined between two surfaces and in the presence of a Poiseuille flow). We see the remarkable cyclic polymer motion observed experimentally, and we show that a simple cross-correlation function can be used to measure the corresponding period of motion. We also propose a new empirical equation relating the magnitude of the shear flow to the amount of chain deformation, an equation that appears to apply for both weak and strong flows. Finally, we report on packing effects near the molecularly flat wall, an associated chain-sticking phenomenon, and the impact of the chain hydrodynamic drag on the local fluid flow.     

NMR study of molecular dynamics in selected hydrophilic polymers

The temperature dependencies of the 1H spin-lattice relaxation times T1 and of the proton NMR second moment M2 in the temperature range from about 90 to 420 K were measured for methyl cellulose, hydroxypropyl cellulose and hydroxypropyl methyl cellulose. The proton spin-lattice relaxation measurements reveal two minima due to the C3 reorientation of the methyl groups of the methoxy, methylenemethoxy or propylene oxide groups and the restricted motion of the segment of the polymer chain. The activation energy barriers for these motions were calculated.     

Polymer dynamics from synthetic polymers to proteins

Starting from the standard model of polymer motion — the Rouse model — we briefly present some key experimental results on the mesoscopic dynamics of polymer systems. We touch the role of topological confinement as expressed in the reptation model and discuss in some more detail processes limiting the confinement. In the second part we relate to some new developments concerning the measurement of large-scale internal dynamics of proteins by neutron spin echo.      

Bubble dynamics in double-stranded DNA

We report the first measurement of the dynamics of bubble formation in double-stranded DNA. Fluctuations of fluorescence of a synthetic DNA construct, internally tagged with a fluorophore and a quencher, are monitored by fluorescence correlation spectroscopy. The relaxation dynamics follow a multistate relaxation kinetics, with a characteristic time scale of 50 microseconds. A simple model of bubble dynamics based on constant zipping-unzipping rates is proposed to account for our experimental data. The role of different secondary structures stabilizing the open bubble is tested.     

DNA dynamics in a microchannel

An extended Brownian dynamics simulation method is used to characterize the dynamics of long DNA molecules flowing in microchannels. The relaxation time increases due to confinement in agreement with scaling predictions. During flow the molecules migrate toward the channel center line, and thereby segregate according to molecular weight. Capturing these effects requires the detailed incorporation of solvent flow in the simulation method, demonstrating the importance of hydrodynamic effects in the dynamics of confined macromolecules.