Session W17: Focus Session: Dynamics of Polymers and Complex Fluids III

Sequence Dependent Electrophoretic Separations of DNA in Pluronic F127 Gels

Two-dimensional (2-D) electrophoresis has successfully been used to visualize the separation of DNA fragments of the same length. We electrophorese a double-stranded DNA ladder in an Agarose gel for the first dimension and in gels of Pluronic F127 for the second dimension at room temperature. The 1000 bp band that travels together as a single band in an Agarose gel is split into two bands in Pluronic gels. The slower band follows the exponential decay trend that the other ladder constituents do. After sequencing the DNA fragments, the faster band has an apparently random sequence, while the slower band and the others have two A-tracts in each 250 bp segment. The A-tracts consist of a series of at least five adenine bases pairing with thymine bases. This result leads to the conclusion that the migration of the DNA molecules bent with A-tracts is more retarded in Pluronic gels than the wild-type of DNA molecules.   

Clusters of Janus Particles in Stokes Flow

In recent years it has become possible to synthesize colloidal particles with anisotropic interactions, which has opened the possibility to control their self-assembly into a variety of superstructures. One of the simplest examples of such ``patchy'' colloids is the Janus particle, a spherical colloid with two chemically distinct hemispheres. If one of these hemispheres is hydrophobic, immersion in an aqueous solvent creates an anisotropic attractive interaction between the hydrophobic hemispheres, driving assembly of these particles into micelle-like clusters. Individual particles also interact anisotropically with the fluid, wherein the surface wetting behavior may manifest as nontrivial translation--rotation coupling. We examine both effects by simulating the formation and dynamical behavior of clusters of Janus particles under uniform Stokes flow utilizing a coarse-grained model of the solvent.   

High Frequency Relaxation in Fluid Mixtures, Protein Solubility and Entropy-Enthalpy Compensation

Additives to polymeric materials can lead to appreciable changes in the rates of relaxation and reaction in these mixtures that can greatly alter material properties and function. Correspondingly, the presence of polymers in solution can significantly affect self-assembly processes essential to living systems and manufacturing applications. This general class of problems is addressed in a specific practical context by developing a virial expansion to describe the influence of polymeric additives on the equilibrium constant governing protein self-assembly and solubility in solution. We find that the well known enhancement of protein self-assembly by polymer additives arising from a modification of the entropy of the assembly by repulsive polymer-protein excluded volume interactions is progressively compensated by attractive polymer-protein interactions that alter the enthalpy of assembly. Equilibrium constants and rate constants for diverse association, reaction, and relaxation processes in condensed state mixtures are amenable to the same type of statistical mechanical treatment so that this entropy-enthalpy compensation effect is predicted to be a rather generic phenomenon. Observations on the high frequency relaxation times of diverse mixtures confirm the generality of this relationship.   

Single-Molecule Studies of DNA Dynamics and Intermolecular Forces

Typically, polymeric fluids are experimentally investigated by examining the bulk properties of the fluid, so the individual molecular dynamics can only be inferred from the fluid properties by using theoretical predictions that relate the two. However, DNA has been shown to be a model system for probing fundamental questions in polymer science, and the recent development of the single-molecule approach using DNA has allowed for direct probing of the molecular conformations and dynamics of polymers. Here, DNA molecules were used to investigate how molecular length, topology and concentration influence the dynamical properties of polymers. Fluorescence microscopy and single-molecule tracking were used to determine self-diffusion coefficients of DNA molecules, and a new experimental approach was developed, using optical tweezers, to measure the intermolecular forces confining entangled DNA molecules. Scaling of diffusion with concentration was determined for the four possible topological combinations of linear and circular molecules. At higher concentrations topology had a dramatic effect on the diffusion, and scaling was in agreement with the reptation model, predicted to describe the dynamics of entangled polymers. The notable exception was the strongly hindered diffusion of a circular molecule in an entangled solution of linear DNA. Using the new optical tweezers method, a tube-like field confining a single entangled molecule was measured, in accord with the key assumption of the reptation model. A time-dependent harmonic potential opposed displacement transverse to the molecular contour, and the force relaxations following displacement were composed of three distinct modes. A characteristic tube radius for the entangled solution was also determined, close to the classically predicted value. The dependence of the above findings on molecular topology and concentration was also investigated.   

Polymer dynamics during capillary flow into nanopores

Ordered arrays of parallel cylindrical nanopores (with a narrow pore size distribution and diameters down to 10 nm) are used as measurement platforms in the field of polymer nano-fluidics, in particular, to investigate the capillary flow of polymers in 2D geometrical nano-confinement. Several aspects of the polymer dynamics -- manifested on time scales covering more than 10 orders of magnitude -- are investigated during the flow process: (i) molecular fluctuations corresponding to the segmental dynamics (dynamic glass transition), (ii) chain dynamics, as revealed -- for the case of type-A polymers -- in fluctuations of the end-to-end distance, (iii) velocity of the capillary flow in dependence on the diameter of the nanopores. The results are compared to the polymer dynamics in the bulk.   

Modification of the coil-stretch transition by confinement

Large double stranded DNA are both a powerful system to study polymer dynamics at the single molecule level and also important molecules for genomic applications. While homogenous electric fields are routinely used to separate DNA in gels, DNA deformation in more complex fields has been less widely studied. We will demonstrate how micro/nanofluidic devices allow for the generation of electric fields with well-defined kinematics for trapping, stretching and then watching DNA relax back to equilibrium. The dimensions of the devices highly confine DNA and subsequently change both their conformation and dynamics. We will show how these confinements effects change the coil-stretch transition of a DNA being electrophoretically stretched in a purely elongational electrical field.~ We experimentally show that a two-stage coil stretch transition occurs and develop a simple dumbbell model which captures most of the relevant physics. We trace the origin of this phenomena to the modification of the effective spring law due to confinement.   

Nanofluidic flow with polymers

We study the behavior of a single polymer in fluid flow in a periodic array of nanopits, which has also been a subject of recent experiments. We employ an explicit solvent based on the lattice Boltzmann method that reproduces the fluctuating Navier-Stokes equation with a well-defined temperature. The fluid functions as a heat bath for the polymer, whose constituents are coupled realistically to the solvent through a frictional force.   

Single-Molecule Tracking of Polymers on Surfaces

Single-molecule tracking technique is, for the first time, applied to study adsorbed polymers on surfaces. Fluorescently-labeled poly (ethylene glycol) (PEG) chains are allowed to freely adsorb from dilute aqueous solutions to various surfaces with different affinity. After rinsing away any non-adsorbed chains, the motion of the surface-bound species is tracked using objective-based total internal reflection fluorescence microscopy (TIRFM). Using our single particle tracking algorithm, individual chain behaviors are analyzed with sub-diffraction resolution.   

Surface Directed Phase Separation and Ordering in Semi-flexible Polymer Solution under Confinement

For a solution of semi-flexible polymers confined between two parallel walls, we study the kinetics of phase separation accompanied by thermally induced ordering in the nematic regime. The mean-field free energy functional is expansion in two order parameters - the conserved local composition and the non-conserved orientation (tensor), with coefficients appropriate for the semi-flexible polymer molecules. By solving the coupled time-dependent Ginzburg-Landau equations for two order parameters, we examine the morphology development and validity of the dynamical scaling in confined geometries in two- dimensions. The homeotropic anchoring at the walls enhances the overall ordering kinetics. The competition between the thermodynamic potential in the bulk and at the surface results into variety of morphological patterns. The role of surface potential in anisotropy of domain growth will be elucidated for a range of polymer concentrations and quench depths.   

Nonmonotonic size dependence of the electrophoretic mobility of stiff and slightly flexible rods in random arrays of obstacles

Using 2D Brownian Dynamics simulations, we study the motion of stiff charged rods in a uniform electric field in arrays of randomly placed obstacles (modeling, e.g., a gel, an entangled polymer solution, or a microfabricated nanopillar array). A long infinitely stiff rod in a strong field can be trapped for a very long time that depends exponentially on both the field strength and the rod length. However, for moderate fields and not too long rods such trapping is rare and the corresponding rate decreases significantly if the rods are slightly flexible or the obstacles are slightly mobile. For this reason, the mobility of untrapped rods is a physically meaningful quantity. This mobility depends nonmonotonically on the rod length, as longer rods orient more along the field and thus collide less with the obstacles. We develop a theory that describes the scaling of the rod orientation and the position of the mobility minimum with all relevant parameters and agrees with our simulation data.   

Fluorescent nanospheres as a probe for confined fluids rheology

Research in the understanding of the dynamics of confined thin films has proved to be challenging. While theoretical models and computer simulations have been developed, few experiments have been performed. One such attempt was the use of well defined geometries with surface forces apparatus (SFA) combined with fluorescence spectroscopies developed in the Granick group. We have extended this technique by incorporating fluorescence imaging and particle tracking within a tribological contact. Nanoparticles and quantum dots were used as our tracers. A sphere on flat geometry was employed and shear was applied. The dynamics of the particles was monitored as they progressed through the contact. The interrelationship between dynamics of confined fluids and their tribological properties was explored. Furthermore, tracers were also used to model how wear particles interact with the contacting surfaces at a tribological contact.   

Life-like functionality and self-organization in a system of communicating polymeric microcapsules

We report the results of computational study of self- organization and life-like functionality in a system of polymeric microcapsules in a fluid-filled microchannel. We consider the case where motion of the nanoparticle-filled microcapsules is controlled by adhesion at the channel’s wall and hydrodynamic coupling between the capsules. Using the hybrid Lattice Boltzmann method for fluid dynamics and Lattice spring model for the micromechanics of elastic solid, we determined how the characteristics of the substrate, the polymeric shell, encapsulated fluid and the surrounding solution affect the capsule's velocity and ``gait'' of the capsule within the system. In numerical computations we locate the conditions, under which microcapsules communicating through modification of the microchannel surface by released nanoparticles exhibit self-organization, thereby mimicking behavior of the colony of living cells. In particular, we show that this system demonstrates collective, directional motion where a group of target microcapsules is led by a single signaling microcapsule. The results of computations provide guidelines for engineering artificial systems with life-like functionality.   

Reduced Interfacial Entanglement Density Affects Boundary Condition of Polymer Flowe

Hydrodynamic boundary conditions play a crucial role in the flow dynamics of thin films and can be probed by the analysis of liquid front profiles. For long-chained polymer films it was reported that a deviation from a symmetric profile is a result of viscoelastic effects. Our experiments show, however, that merely a slip boundary condition at the solid/liquid interface can lead to an asymmetric profile. Variation of molecular weight shows that slippage is directly linked to chain entanglements. We find a reduced entanglement density at the solid/liquid interface (factor 3 to 4), which stresses the importance of considering non-bulk polymer properties in the vicinity of an interface. [O. Baumchen, R. Fetzer and K. Jacobs, Phys. Rev. Lett. (in press).]