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

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

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

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

A Neutral Polyampholyte in an ionic solution

The behavior of a neutral polyampholyte ($PA$) chain with $N$ monomers, in an ionic solution, is analyzed in the framework of the full Debye-H$\ddot u$ckel-Bjerrum-Flory $(DHBjF)$ theory. A $PA$ chain, that in addition to the neutral monomers, also contains an equal number of positively and negatively charged monomers, is dissolved in an ionic solution. For \underline{high} concentrations of salt and at high temperatures, the $PA$ exists in an extended state. As the temperature is decreased, the electrostatic energy becomes more relevant and at a $T=T_{\theta}$ the system collapses into a dilute globular state, or microelectrolyte. This state contains a concentration of salt higher than the surrounding medium. As the temperature is decreased even further, association between the monomers of the polymer and the ions of the salt becomes relevant and there is a crossover from this globular state to a low temperature extended state. For \underline{low} densities of salt, the system is collapsed for almost all temperatures and exhibits a first-order phase transition to an extended state at an unphysical low temperature.Comment: 10 pages, Revtex with epsf, 9 Postscript figures. Submitted to PR

Tension Dynamics and Linear Viscoelastic Behavior of a Single Semiflexible Polymer Chain

We study the dynamical response of a single semiflexible polymer chain based on the theory developed by Hallatschek et al. for the wormlike-chain model. The linear viscoelastic response under oscillatory forces acting at the two chain ends is derived analytically as a function of the oscillation frequency . We shall show that the real part of the complex compliance in the low frequency limit is consistent with the static result of Marko and Siggia whereas the imaginary part exhibits the power-law dependence +1/2. On the other hand, these compliances decrease as the power law -7/8 for the high frequency limit. These are different from those of the Rouse dynamics. A scaling argument is developed to understand these novel results.Comment: 23 pages, 6 figure

Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach