DNA uptake into nuclei: Numerical and analytical results

The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake into the cell nucleus, a phenomenon experimentally investigated by attaching a small bead to the free end of the double helix and pulling this bead with the help of an optical trap. The experiments show that the uptake is monotonous and slows down when the remaining DNA segment becomes very short. Numerical and analytical studies of the entropic repulsion between the DNA filament and the membrane wall suggest a new interpretation of the experimental observations. Our results indicate that the repulsion monotonically decreases as the uptake progresses. Thus, the DNA is pulled in (i) either by a small force of unknown origin, and then the slowing down can be interpreted only statistically; (ii) or by a strong but slow ratchet mechanism, which would naturally explain the observed monotonicity, but then the slowing down requires additional explanations. Only further experiments can unambiguously distinguish between these two mechanisms.Comment: 12 pages, 6 figures, submitted to J. Phys. Cond. Ma

Microscopic theory of network glasses

A molecular theory of the glass transition of network forming liquids is developed using a combination of self-consistent phonon and liquid state approaches. Both the dynamical transition and the entropy crisis characteristic of random first order transitions are mapped out as a function of the degree of bonding and the density. Using a scaling relation for a soft-core model to crudely translate the densities into temperatures, the theory predicts that the ratio of the dynamical transition temperature to the laboratory transition temperature rises as the degree of bonding increases, while the Kauzmann temperature falls relative to the laboratory transition. These results indicate why highly coordinated liquids should be "strong" while van der Waals liquids without coordination are "fragile".Comment: slightly revised version that has been accepted for publication in Phys. Rev. Let

Elasticity model of a supercoiled DNA molecule

Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral representation for a quantum charged particle in the field of a magnetic monopole with unquantized charge. We show that the theory is singular in the continuum limit and must be regularised at an intermediate length scale. We find good agreement with existing experimental data, and point out how to measure the twist rigidity accurately.Comment: Latex, 4 pages. The figure contains new experimental data, giving a new determination of the twist rigidit

Elasticity of Semiflexible Biopolymer Networks

We develop a model for gels and entangled solutions of semiflexible biopolymers such as F-actin. Such networks play a crucial structural role in the cytoskeleton of cells. We show that the rheologic properties of these networks can result from nonclassical rubber elasticity. This model can explain a number of elastic properties of such networks {\em in vitro}, including the concentration dependence of the storage modulus and yield strain.Comment: Uses RevTeX, full postscript with figures available at http://www.umich.edu/~fcm/preprints/agel/agel.htm

Diffusion with random distribution of static traps

The random walk problem is studied in two and three dimensions in the presence of a random distribution of static traps. An efficient Monte Carlo method, based on a mapping onto a polymer model, is used to measure the survival probability P(c,t) as a function of the trap concentration c and the time t. Theoretical arguments are presented, based on earlier work of Donsker and Varadhan and of Rosenstock, why in two dimensions one expects a data collapse if -ln[P(c,t)]/ln(t) is plotted as a function of (lambda t)^{1/2}/ln(t) (with lambda=-ln(1-c)), whereas in three dimensions one expects a data collapse if -t^{-1/3}ln[P(c,t)] is plotted as a function of t^{2/3}lambda. These arguments are supported by the Monte Carlo results. Both data collapses show a clear crossover from the early-time Rosenstock behavior to Donsker-Varadhan behavior at long times.Comment: 4 pages, 6 figure

Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles

We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness of the molecular setup moderately enhances the signal-to-noise ratio (SNR) in hopping experiments as compared to conventional long handles constructs (approximately 700 bp). The shorter construct results in a signal of higher SNR and slower folding/unfolding kinetics, thereby facilitating the detection of otherwise fast structural transitions. A novel analysis of the elastic properties of the molecular setup, based on high-bandwidth measurements of force fluctuations along the folded branch, reveals that the highest SNR that can be achieved with short handles is potentially limited by the marked reduction of the effective persistence length and stretch modulus of the short linker complex.Comment: Main paper: 20 pages and 6 figures. Supplementary Material: 25 page

Conformations of Linear DNA

We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link number. We derive a fundamental relation between the Euler angles that describe the curve and the topological linking number. Analytical expressions for the spatial configurations of the molecule in the infinite- length limit were obtained. A unique configuraion minimizes the energy for a given set of physical conditions. An elastic model incorporating thermal fluctuations provides excellent agreement with experimental results on the plectonemic transition.Comment: 5 pages, RevTeX; 6 postscript figure

Colloid-Induced Polymer Compression

We consider a model mixture of hard colloidal spheres and non-adsorbing polymer chains in a theta solvent. The polymer component is modelled as a polydisperse mixture of effective spheres, mutually noninteracting but excluded from the colloids, with radii that are free to adjust to allow for colloid-induced compression. We investigate the bulk fluid demixing behaviour of this model system using a geometry-based density-functional theory that includes the polymer size polydispersity and configurational free energy, obtained from the exact radius-of-gyration distribution for an ideal (random-walk) chain. Free energies are computed by minimizing the free energy functional with respect to the polymer size distribution. With increasing colloid concentration and polymer-to-colloid size ratio, colloidal confinement is found to increasingly compress the polymers. Correspondingly, the demixing fluid binodal shifts, compared to the incompressible-polymer binodal, to higher polymer densities on the colloid-rich branch, stabilizing the mixed phase.Comment: 14 pages, 4 figure

Corrections to scaling in 2--dimensional polymer statistics

Writing $= AN^{2\nu}(1+BN^{-\Delta_1}+CN^{-1}+ ...)$ for the mean square end--to--end length $$ of a self--avoiding polymer chain of $N$ links, we have calculated $\Delta_1$ for the two--dimensional {\em continuum} case from a new {\em finite} perturbation method based on the ground state of Edwards self consistent solution which predicts the (exact) $\nu=3/4$ exponent. This calculation yields $\Delta_1=1/2$. A finite size scaling analysis of data generated for the continuum using a biased sampling Monte Carlo algorithm supports this value, as does a re--analysis of exact data for two--dimensional lattices.Comment: 10 pages of RevTex, 5 Postscript figures. Accepted for publication in Phys. Rev. B. Brief Reports. Also submitted to J. Phys.

Elasticity of semiflexible polymers with and without self-interactions

A {\it new} formula for the force vs extension relation is derived from the discrete version of the so called {\it worm like chain} model. This formula correctly fits some recent experimental data on polymer stretching and some numerical simulations with pairwise repulsive potentials. For a more realistic Lennard-Jones potential the agreement with simulations is found to be good when the temperature is above the $\theta$ temperature. For lower temperatures a plateau emerges, as predicted by some recent experimental and theoretical results, and our formula gives good results only in the high force regime. We briefly discuss how other kinds of self-interactions are expected to affect the elasticity of the polymer.Comment: 8 pages, 10 figure