Force induced stretched state: Effects of temperature

A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension (reaction co-ordinate) may increase or decrease with the temperature depending upon the applied force. The simple model developed here which incorporates semi-microscopic details of base direction provide an explanation of the force induced transitions in ssDNA as observed in experiments.Comment: 5 pages, 8 figures, RevTex

Searching for cavities of various densities in the Earth's crust with a low-energy electron-antineutrino beta-beam

We propose searching for deep underground cavities of different densities in the Earth's crust using a long-baseline electron-antineutrino disappearance experiment, realized through a low-energy beta-beam with highly-enhanced luminosity. We focus on four cases: cavities with densities close to that of water, iron-banded formations, heavier mineral deposits, and regions of abnormal charge accumulation that have been posited to appear prior to the occurrence of an intense earthquake. The sensitivity to identify cavities attains confidence levels higher than $3\sigma$ and $5\sigma$ for exposures times of 3 months and 1.5 years, respectively, and cavity densities below 1 g cm$^{-3}$ or above 5 g cm$^{-3}$, with widths greater than 200 km. We reconstruct the cavity density, width, and position, assuming one of them known while keeping the other two free. We obtain large allowed regions that improve as the cavity density differs more from the Earth's mean density. Furthermore, we demonstrate that knowledge of the cavity density is important to obtain O(10%) error on the width. Finally, we introduce an observable to quantify the presence of a cavity by changing the orientation of the electron-antineutrino beam, with which we are able to identify the presence of a cavity at the $2\sigma$ to $5\sigma$ C.L.Comment: 7 pages, 5 figures; matches published versio

A family of Nikishin systems with periodic recurrence coefficients

Suppose we have a Nikishin system of $p$ measures with the $k$th generating measure of the Nikishin system supported on an interval \Delta_k\subset\er with $\Delta_k\cap\Delta_{k+1}=\emptyset$ for all $k$. It is well known that the corresponding staircase sequence of multiple orthogonal polynomials satisfies a $(p+2)$-term recurrence relation whose recurrence coefficients, under appropriate assumptions on the generating measures, have periodic limits of period $p$. (The limit values depend only on the positions of the intervals $\Delta_k$.) Taking these periodic limit values as the coefficients of a new $(p+2)$-term recurrence relation, we construct a canonical sequence of monic polynomials $\{P_{n}\}_{n=0}^{\infty}$, the so-called \emph{Chebyshev-Nikishin polynomials}. We show that the polynomials $P_{n}$ themselves form a sequence of multiple orthogonal polynomials with respect to some Nikishin system of measures, with the $k$th generating measure being absolutely continuous on $\Delta_{k}$. In this way we generalize a result of the third author and Rocha \cite{LopRoc} for the case $p=2$. The proof uses the connection with block Toeplitz matrices, and with a certain Riemann surface of genus zero. We also obtain strong asymptotics and an exact Widom-type formula for the second kind functions of the Nikishin system for $\{P_{n}\}_{n=0}^{\infty}$.Comment: 30 pages, minor change

Force dependent fragility in RNA hairpins

We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using laser tweezers. We identify two different kinetic regimes depending on the range of forces explored during the unfolding and refolding process. The present approach extends the range of validity of the two-states approximation by providing a theoretical framework to reconstruct free-energy landscapes and identify force-induced structural changes in molecular transition states using single molecule pulling experiments. The method should be applicable to RNA hairpins with multiple kinetic barriers.Comment: Latex file, 4 pages+3 figure

FKBP5 DNA methylation does not mediate the association between childhood maltreatment and depression symptom severity in the Detroit Neighborhood Health Study

Exposure to childhood maltreatment increases the risk of developing mental illness later in life. Childhood maltreatment and depression have both been associated with dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis—a key regulator of the body's stress response. Additionally, HPA axis dysregulation has been implicated in the etiology of a range of mental illnesses. A substantial body of work has shown history of childhood maltreatment alters DNA methylation levels within key HPA axis genes. We therefore investigated whether one of these key genes, FKBP5 mediates the relationship between childhood maltreatment and depression, and assessed FKBP5 DNA methylation and gene expression within 112 adults from the Detroit Neighborhood Health Study (DNHS). DNA methylation was assessed in 4 regions, including the upstream promoter, downstream promoter, and two glucocorticoid response elements (GREs) via pyrosequencing using whole blood derived DNA; Taqman assays measured relative RNA expression from leukocytes. Mediation analyses were conducted using sequential linear regression. Childhood maltreatment was significantly associated with depression symptom severity (FDR 0.05). Our results suggest DNA methylation does not mediate the childhood maltreatment-depression association in the DNHS

Ideal evolution of MHD turbulence when imposing Taylor-Green symmetries

We investigate the ideal and incompressible magnetohydrodynamic (MHD) equations in three space dimensions for the development of potentially singular structures. The methodology consists in implementing the four-fold symmetries of the Taylor-Green vortex generalized to MHD, leading to substantial computer time and memory savings at a given resolution; we also use a re-gridding method that allows for lower-resolution runs at early times, with no loss of spectral accuracy. One magnetic configuration is examined at an equivalent resolution of $6144^3$ points, and three different configurations on grids of $4096^3$ points. At the highest resolution, two different current and vorticity sheet systems are found to collide, producing two successive accelerations in the development of small scales. At the latest time, a convergence of magnetic field lines to the location of maximum current is probably leading locally to a strong bending and directional variability of such lines. A novel analytical method, based on sharp analysis inequalities, is used to assess the validity of the finite-time singularity scenario. This method allows one to rule out spurious singularities by evaluating the rate at which the logarithmic decrement of the analyticity-strip method goes to zero. The result is that the finite-time singularity scenario cannot be ruled out, and the singularity time could be somewhere between $t=2.33$ and $t=2.70.$ More robust conclusions will require higher resolution runs and grid-point interpolation measurements of maximum current and vorticity.Comment: 18 pages, 13 figures, 2 tables; submitted to Physical Review

A two-parameter random walk with approximate exponential probability distribution

We study a non-Markovian random walk in dimension 1. It depends on two parameters eps_r and eps_l, the probabilities to go straight on when walking to the right, respectively to the left. The position x of the walk after n steps and the number of reversals of direction k are used to estimate eps_r and eps_l. We calculate the joint probability distribution p_n(x,k) in closed form and show that, approximately, it belongs to the exponential family.Comment: 12 pages, updated reference to companion paper cond-mat/060126