DNA Spools under Tension

DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two puzzling and seemingly unrelated recent experimental findings, the sudden quantized unwrapping of nucleosomes and that of DNA toroidal condensates under tension are theoretically explained and shown to be of the same origin. The study provides new insights into nucleosome and chromatin fiber stability and dynamics

Facet Formation in the Negative Quenched Kardar-Parisi-Zhang Equation

The quenched Kardar-Parisi-Zhang (QKPZ) equation with negative non-linear term shows a first order pinning-depinning (PD) transition as the driving force $F$ is varied. We study the substrate-tilt dependence of the dynamic transition properties in 1+1 dimensions. At the PD transition, the pinned surfaces form a facet with a characteristic slope $s_c$ as long as the substrate-tilt $m$ is less than $s_c$. When $m<s_c$, the transition is discontinuous and the critical value of the driving force $F_c(m)$ is independent of $m$, while the transition is continuous and $F_c(m)$ increases with $m$ when $m>s_c$. We explain these features from a pinning mechanism involving a localized pinning center and the self-organized facet formation.Comment: 4 pages, source TeX file and 7 PS figures are tarred and compressed via uufile

Molecular Weight Dependence of Spreading Rates of Ultrathin Polymeric Films

We study experimentally the molecular weight $M$ dependence of spreading rates of molecularly thin precursor films, growing at the bottom of droplets of polymer liquids. In accord with previous observations, we find that the radial extension R(t) of the film grows with time as R(t) = (D_{exp} t)^{1/2}. Our data substantiate the M-dependence of D_{exp}; we show that it follows D_{exp} \sim M^{-\gamma}, where the exponent \gamma is dependent on the chemical composition of the solid surface, determining its frictional properties with respect to the molecular transport. In the specific case of hydrophilic substrates, the frictional properties can be modified by the change of the relative humidity (RH). We find that \gamma \approx 1 at low RH and tends to zero when RH gets progressively increased. We propose simple theoretical arguments which explain the observed behavior in the limits of low and high RH.Comment: 4 pages, 2 figures, to appear in PR

Angles from BB Decays with Charm

Proceedings of the CKM 2005 Workshop (WG5), UC San Diego, 15-18 March 2005.Comment: 62 pages, 55 figures. Proceedings of the CKM 2005 Workshop (WG5), UC San Diego, 15-18 March 200

Fluctuation-Facilitated Charge Migration along DNA

We propose a model Hamiltonian for charge transfer along the DNA double helix with temperature driven fluctuations in the base pair positions acting as the rate limiting factor for charge transfer between neighboring base pairs. We compare the predictions of the model with the recent work of J.K. Barton and A.H. Zewail (Proc.Natl.Acad.Sci.USA, {\bf 96}, 6014 (1999)) on the unusual two-stage charge transfer of DNA.Comment: 4 pages, 2 figure

Nonequilibrium dynamics of random field Ising spin chains: exact results via real space RG

Non-equilibrium dynamics of classical random Ising spin chains are studied using asymptotically exact real space renormalization group. Specifically the random field Ising model with and without an applied field (and the Ising spin glass (SG) in a field), in the universal regime of a large Imry Ma length so that coarsening of domains after a quench occurs over large scales. Two types of domain walls diffuse in opposite Sinai random potentials and mutually annihilate. The domain walls converge rapidly to a set of system-specific time-dependent positions {\it independent of the initial conditions}. We obtain the time dependent energy, magnetization and domain size distribution (statistically independent). The equilibrium limits agree with known exact results. We obtain exact scaling forms for two-point equal time correlation and two-time autocorrelations. We also compute the persistence properties of a single spin, of local magnetization, and of domains. The analogous quantities for the spin glass are obtained. We compute the two-point two-time correlation which can be measured by experiments on spin-glass like systems. Thermal fluctuations are found to be dominated by rare events; all moments of truncated correlations are computed. The response to a small field applied after waiting time $t_w$, as measured in aging experiments, and the fluctuation-dissipation ratio $X(t,t_w)$ are computed. For $(t-t_w) \sim t_w^{\hat{\alpha}}$, $\hat{\alpha} <1$, it equals its equilibrium value X=1, though time translational invariance fails. It exhibits for $t-t_w \sim t_w$ aging regime with non-trivial $X=X(t/t_w) \neq 1$, different from mean field.Comment: 55 pages, 9 figures, revte

Vibrational Enhancement of the Effective Donor - Acceptor Coupling

The paper deals with a simple three sites model for charge transfer phenomena in an one-dimensional donor (D) - bridge (B) - acceptor (A) system coupled with vibrational dynamics of the B site. It is found that in a certain range of parameters the vibrational coupling leads to an enhancement of the effective donor - acceptor electronic coupling as a result of the formation of the polaron on the B site. This enhancement of the charge transfer efficiency is maximum at the resonance, where the effective energy of the fluctuating B site coincides with the donor (acceptor) energy.Comment: 5 pages, 3 figure

The depinning transition of a driven interface in the random-field Ising model around the upper critical dimension

We investigate the depinning transition for driven interfaces in the random-field Ising model for various dimensions. We consider the order parameter as a function of the control parameter (driving field) and examine the effect of thermal fluctuations. Although thermal fluctuations drive the system away from criticality the order parameter obeys a certain scaling law for sufficiently low temperatures and the corresponding exponents are determined. Our results suggest that the so-called upper critical dimension of the depinning transition is five and that the systems belongs to the universality class of the quenched Edward-Wilkinson equation.Comment: accepted for publication in Phys. Rev.

Dynamic Scaling of Ion-Sputtered Surfaces

We derive a stochastic nonlinear equation to describe the evolution and scaling properties of surfaces eroded by ion bombardment. The coefficients appearing in the equation can be calculated explicitly in terms of the physical parameters characterizing the sputtering process. We find that transitions may take place between various scaling behaviors when experimental parameters such as the angle of incidence of the incoming ions or their average penetration depth, are varied.Comment: 13 pages, Revtex, 2 figure

Intermittency in Dynamics of Two-Dimensional Vortex-like Defects

We examine high-order dynamical correlations of defects (vortices, disclinations etc) in thin films starting from the Langevin equation for the defect motion. We demonstrate that dynamical correlation functions $F_{2n}$ of vorticity and disclinicity behave as $F_{2n}\sim y^2/r^{4n}$ where $r$ is the characteristic scale and $y$ is the fugacity. As a consequence, below the Berezinskii-Kosterlitz-Thouless transition temperature $F_{2n}$ are characterized by anomalous scaling exponents. The behavior strongly differs from the normal law $F_{2n}\sim F_2^n$ occurring for simultaneous correlation functions, the non-simultaneous correlation functions appear to be much larger. The phenomenon resembles intermittency in turbulence.Comment: 30 pages, 11 figure