Theory of High-Force DNA Stretching and Overstretching

Single molecule experiments on single- and double stranded DNA have sparked a renewed interest in the force-extension of polymers. The extensible Freely Jointed Chain (FJC) model is frequently invoked to explain the observed behavior of single-stranded DNA. We demonstrate that this model does not satisfactorily describe recent high-force stretching data. We instead propose a model (the Discrete Persistent Chain, or ``DPC'') that borrows features from both the FJC and the Wormlike Chain, and show that it resembles the data more closely. We find that most of the high-force behavior previously attributed to stretch elasticity is really a feature of the corrected entropic elasticity; the true stretch compliance of single-stranded DNA is several times smaller than that found by previous authors. Next we elaborate our model to allow coexistence of two conformational states of DNA, each with its own stretch and bend elastic constants. Our model is computationally simple, and gives an excellent fit through the entire overstretching transition of nicked, double-stranded DNA. The fit gives the first values for the elastic constants of the stretched state. In particular we find the effective bend stiffness for DNA in this state to be about 10 nm*kbt, a value quite different from either B-form or single-stranded DNAComment: 33 pages, 11 figures. High-quality figures available upon reques

Modulational instability in periodic quadratic nonlinear materials

We investigate the modulational instability of plane waves in quadratic nonlinear materials with linear and nonlinear quasi-phase-matching gratings. Exact Floquet calculations, confirmed by numerical simulations, show that the periodicity can drastically alter the gain spectrum but never completely removes the instability. The low-frequency part of the gain spectrum is accurately predicted by an averaged theory and disappears for certain gratings. The high-frequency part is related to the inherent gain of the homogeneous non-phase-matched material and is a consistent spectral feature.Comment: 4 pages, 7 figures corrected minor misprint

Complete Set of Polarization Transfer Observables for the 12C(p,n)^{12}{\rm C}(p,n) Reaction at 296 MeV and 0∘^{\circ}

A complete set of polarization transfer observables has been measured for the $^{12}{\rm C}(p,n)$ reaction at $T_p=296 {\rm MeV}$ and $\theta_{\rm lab}=0^{\circ}$. The total spin transfer $\Sigma(0^{\circ})$ and the observable $f_1$ deduced from the measured polarization transfer observables indicate that the spin--dipole resonance at $E_x \simeq 7 {\rm MeV}$ has greater $2^-$ strength than $1^-$ strength, which is consistent with recent experimental and theoretical studies. The results also indicate a predominance of the spin-flip and unnatural-parity transition strength in the continuum. The exchange tensor interaction at a large momentum transfer of $Q \simeq 3.6 {\rm fm}^{-1}$ is discussed.Comment: 4 pages, 4 figure

Parametric localized modes in quadratic nonlinear photonic structures

We analyze two-color spatially localized modes formed by parametrically coupled fundamental and second-harmonic fields excited at quadratic (or chi-2) nonlinear interfaces embedded into a linear layered structure --- a quasi-one-dimensional quadratic nonlinear photonic crystal. For a periodic lattice of nonlinear interfaces, we derive an effective discrete model for the amplitudes of the fundamental and second-harmonic waves at the interfaces (the so-called discrete chi-2 equations), and find, numerically and analytically, the spatially localized solutions --- discrete gap solitons. For a single nonlinear interface in a linear superlattice, we study the properties of two-color localized modes, and describe both similarities and differences with quadratic solitons in homogeneous media.Comment: 9 pages, 8 figure

Absolute dimensions of the unevolved B-type eclipsing binary GG Orionis

We present photometric observations in B and V as well as spectroscopic observations of the detached, eccentric 6.6-day double-lined eclipsing binary GG Ori, a member of the Orion OB1 association. Absolute dimensions of the components, which are virtually identical, are determined to high accuracy (better than 1% in the masses and better than 2% in the radii) for the purpose of testing various aspects of theoretical modeling. We obtain M(A) = 2.342 +/- 0.016 solar masses and R(A) = 1.852 +/- 0.025 solar radii for the primary, and M(B) = 2.338 +/- 0.017 solar masses and R(B) = 1.830 +/- 0.025 solar radii for the secondary. The effective temperature of both stars is 9950 +/- 200 K, corresponding to a spectral type of B9.5. GG Ori is very close to the ZAMS, and comparison with current stellar evolution models gives ages of 65-82 Myr or 7.7 Myr depending on whether the system is considered to be burning hydrogen on the main sequence or still in the final stages of pre-main sequence contraction. We have detected apsidal motion in the binary at a rate of dw/dt = 0.00061 +/- 0.00025 degrees per cycle, corresponding to an apsidal period of U = 10700 +/- 4500 yr. A substantial fraction of this (approximately 70%) is due to the contribution from General Relativity.Comment: To appear in The Astronomical Journal, December 200

Mesoscopic models for DNA stretching under force: new results and comparison to experiments

Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity. It has been proposed that the first transition, at forces of 60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA, while the second one, at stronger forces, is a strand peeling resulting in single stranded DNAs (ssDNA), similar to thermal denaturation. But due to experimental conditions these two transitions can overlap, for instance for poly(dA-dT). We derive analytical formula using a coupled discrete worm like chain-Ising model. Our model takes into account bending rigidity, discreteness of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit of zero force, this model simplifies into a coupled model already developed by us for studying thermal DNA melting, establishing a connexion with previous fitting parameter values for denaturation profiles. We find that: (i) ssDNA is fitted, using an analytical formula, over a nanoNewton range with only three free parameters, the contour length, the bending modulus and the monomer size; (ii) a surprisingly good fit on this force range is possible only by choosing a monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss) transitions; (iv) an analytical formula for fitting B to S transitions is derived in the strong force approximation and for long DNAs, which is in excellent agreement with exact transfer matrix calculations; (v) this formula fits perfectly well poly(dG-dC) and $\lambda$-DNA force-extension curves with consistent parameter values; (vi) a coherent picture, where S to ssDNA transitions are much more sensitive to base-pair sequence than the B to S one, emerges.Comment: 14 pages, 9 figure

Quantum state engineering assisted by entanglement

We suggest a general scheme for quantum state engineering based on conditional measurements carried out on entangled twin-beam of radiation. Realistic detection schemes such as {\sc on/off} photodetection, homodyne detection and joint measurement of two-mode quadratures are analyzed in details. Imperfections of the apparatuses, such as nonunit quantum efficiency and finite resolution, are taken into account. We show that conditional {\sc on/off} photodetection provides a reliable scheme to verify nonclassicality, whereas conditional homodyning represents a tunable and robust source of squeezed light. We also describe optical teleportation as a conditional measurement, and evaluate the degrading effects of finite amount of entanglement, decoherence due to losses, and nonunit quantum efficiency.Comment: Some pics with low resolution. Originals at http://www.qubit.i

Single Molecule Statistics and the Polynucleotide Unzipping Transition

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force value of order 10 pN, with different critical behavior for homopolymers and for random heteropolymers. We extend results on the disorder-averaged behavior of DNA's with random sequences to the more experimentally accessible problem of unzipping a single DNA molecule. As the applied force approaches the critical value, the double-stranded DNA unravels in a series of discrete, sequence-dependent steps that allow it to reach successively deeper energy minima. Plots of extension versus force thus take the striking form of a series of plateaus separated by sharp jumps. Similar qualitative features should reappear in micromanipulation experiments on proteins and on folded RNA molecules. Despite their unusual form, the extension versus force curves for single molecules still reveal remnants of the disorder-averaged critical behavior. Above the transition, the dynamics of the unzipping fork is related to that of a particle diffusing in a random force field; anomalous, disorder-dominated behavior is expected until the applied force exceeds the critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure

Artificial drainage of peatlands: hydrological and hydrochemical process and wetland restoration

Peatlands have been subject to artificial drainage for centuries. This drainage has been in response to agricultural demand, forestry, horticultural and energy properties of peat and alleviation of flood risk. However, the are several environmental problems associated with drainage of peatlands. This paper describes the nature of these problems and examines the evidence for changes in hydrological and hydrochemical processes associated with these changes. Traditional black-box water balance approaches demonstrate little about wetland dynamics and therefore the science of catchment response to peat drainage is poorly understood. It is crucial that a more process-based approach be adopted within peatland ecosystems. The environmental problems associated with peat drainage have led, in part, to a recent reversal in attitudes to peatlands and we have seen a move towards wetland restoration. However, a detailed understanding of hydrological, hydrochemical and ecological process-interactions will be fundamental if we are to adequately restore degraded peatlands, preserve those that are still intact and understand the impacts of such management actions at the catchment scale