Effects of Kinks on DNA Elasticity

We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of trans-gauche rotations in the backbone of the single-stranded DNA. The problem is solved both analytically and numerically by generalizing the well-known analogy to the Quantum Rotator. In the small stretching force regime, we find that the persistence length is renormalized due to the presence of the kinks. In the opposite regime, the response to the strong stretching is determined solely by the bare persistence length with exponential corrections due to the ``ideal gas of kinks''. This high-force behavior changes significantly in the limit of high bending rigidity of the chain. In that case, the leading corrections to the mechanical response are likely to be due to the formation of multi-kink structures, such as kink pairs.Comment: v1: 16 pages, 7 figures, LaTeX; submitted to Physical Review E; v2: a new subsection on soft kinks added to section Theory, sections Introduction and Conclusions expanded, references added, other minor changes; v3: a reference adde

Scientific basis for safely shutting in the Macondo Well after the April 20, 2010 Deepwater Horizon blowout

As part of the government response to the Deepwater Horizon blowout, a Well Integrity Team evaluated the geologic hazards of shutting in the Macondo Well at the seafloor and determined the conditions under which it could safely be undertaken. Of particular concern was the possibility that, under the anticipated high shut-in pressures, oil could leak out of the well casing below the seafloor. Such a leak could lead to new geologic pathways for hydrocarbon release to the Gulf of Mexico. Evaluating this hazard required analyses of 2D and 3D seismic surveys, seafloor bathymetry, sediment properties, geophysical well logs, and drilling data to assess the geological, hydrological, and geomechanical conditions around the Macondo Well. After the well was successfully capped and shut in on July 15, 2010, a variety of monitoring activities were used to assess subsurface well integrity. These activities included acquisition of wellhead pressure data, marine multichannel seismic pro- files, seafloor and water-column sonar surveys, and wellhead visual/acoustic monitoring. These data showed that the Macondo Well was not leaking after shut in, and therefore, it could remain safely shut until reservoir pressures were suppressed (killed) with heavy drilling mud and the well was sealed with cement

Non-linear complex principal component analysis of nearshore bathymetry

International audienceComplex principal component analysis (CPCA) is a useful linear method for dimensionality reduction of data sets characterized by propagating patterns, where the CPCA modes are linear functions of the complex principal component (CPC), consisting of an amplitude and a phase. The use of non-linear methods, such as the neural-network based circular non-linear principal component analysis (NLPCA.cir) and the recently developed non-linear complex principal component analysis (NLCPCA), may provide a more accurate description of data in case the lower-dimensional structure is non-linear. NLPCA.cir extracts non-linear phase information without amplitude variability, while NLCPCA is capable of extracting both. NLCPCA can thus be viewed as a non-linear generalization of CPCA. In this article, NLCPCA is applied to bathymetry data from the sandy barred beaches at Egmond aan Zee (Netherlands), the Hasaki coast (Japan) and Duck (North Carolina, USA) to examine how effective this new method is in comparison to CPCA and NLPCA.cir in representing propagating phenomena. At Duck, the underlying low-dimensional data structure is found to have linear phase and amplitude variability only and, accordingly, CPCA performs as well as NLCPCA. At Egmond, the reduced data structure contains non-linear spatial patterns (asymmetric bar/trough shapes) without much temporal amplitude variability and, consequently, is about equally well modelled by NLCPCA and NLPCA.cir. Finally, at Hasaki, the data structure displays not only non-linear spatial variability but also considerably temporal amplitude variability, and NLCPCA outperforms both CPCA and NLPCA.cir. Because it is difficult to know the structure of data in advance as to which one of the three models should be used, the generalized NLCPCA model can be used in each situation

Atomic Interferometer with Amplitude Gratings of Light and its Applications to Atom Based Tests of the Equivalence Principle

We have developed a matter wave interferometer based on the diffraction of atoms from effective absorption gratings of light. In a setup with cold rubidium atoms in an atomic fountain the interferometer has been used to carry out tests of the equivalence principle on an atomic basis. The gravitational acceleration of the two isotopes 85Rb and 87Rb was compared, yielding a difference Dg/g =(1.2 +-1.7)x10^{-7}. We also perform a differential free fall measurement of atoms in two different hyperfine states, and obtained a result of Dg/g =(0.4 +-1.2)x10^{-7}.Comment: 4 Pages, 4 figures, accepted for Physical Review Letter

Study of HST counterparts to Chandra X-ray sources in the Globular Cluster M71

We report on archival Hubble Space Telescope (HST) observations of the globular cluster M71 (NGC 6838). These observations, covering the core of the globular cluster, were performed by the Advanced Camera for Surveys (ACS) and the Wide Field Planetary Camera 2 (WFPC2). Inside the half-mass radius (r_h = 1.65') of M71, we find 33 candidate optical counterparts to 25 out of 29 Chandra X-ray sources while outside the half-mass radius, 6 possible optical counterparts to 4 X-ray sources are found. Based on the X-ray and optical properties of the identifications, we find 1 certain and 7 candidate cataclysmic variables (CVs). We also classify 2 and 12 X-ray sources as certain and potential chromospherically active binaries (ABs), respectively. The only star in the error circle of the known millisecond pulsar (MSP) is inconsistent with being the optical counterpart. The number of X-ray faint sources with L_x>4x10^{30} ergs/s (0.5-6.0 keV) found in M71 is higher than extrapolations from other clusters on the basis of either collision frequency or mass. Since the core density of M71 is relatively low, we suggest that those CVs and ABs are primordial in origin.Comment: 12 pages, 6 figures. Accepted for publication in Astronomy and Astrophysic

Controlled Delivery of Sdf-1 Alpha and Igf-1: Cxcr4(+) Cell Recruitment and Functional Skeletal Muscle Recovery

Therapeutic delivery of regeneration-promoting biological factors directly to the site of injury has demonstrated its efficacy in various injury models. Several reports describe improved tissue regeneration following local injection of tissue specific growth factors, cytokines and chemokines. Evidence exists that combined cytokine/growth factor treatment is superior for optimizing tissue repair by targeting different aspects of the regeneration response. The purpose of this study was to evaluate the therapeutic potential of the controlled delivery of stromal cell-derived factor-1alpha (SDF-1 alpha) alone or in combination with insulin-like growth factor-I (SDF-1 alpha/IGF-I) for the treatment of tourniquet-induced ischemia/reperfusion injury (TK-I/R) of skeletal muscle. We hypothesized that SDF-1 alpha will promote sustained stem cell recruitment to the site of muscle injury, while IGF-I will induce progenitor cell differentiation to effectively restore muscle contractile function after TK-I/R injury while concurrently reducing apoptosis. Utilizing a novel poly-ethylene glycol PEGylated fibrin gel matrix (PEG-Fib), we incorporated SDF-1 alpha alone (PEG-Fib/SDF-1 alpha) or in combination with IGF-I (PEG-Fib/SDF-1 alpha/IGF-I) for controlled release at the site of acute muscle injury. Despite enhanced cell recruitment and revascularization of the regenerating muscle after SDF-1 alpha treatment, functional analysis showed no benefit from PEG-Fib/SDF-1 alpha therapy, while dual delivery of PEG-Fib/SDF-1 alpha/IGF-I resulted in IGF-I-mediated improvement of maximal force recovery and SDF-1 alpha-driven in vivo neovasculogenesis. Histological data supported functional data, as well as highlighted the important differences in the regeneration process among treatment groups. This study provides evidence that while revascularization may be necessary for maximizing muscle force recovery, without modulation of other effects of inflammation it is insufficient.Kinesiology and Health Educatio

Volume Fractions of the Kinematic "Near-Critical" Sets of the Quantum Ensemble Control Landscape

An estimate is derived for the volume fraction of a subset $C_{\epsilon}^{P} = \{U : ||grad J(U)|\leq {\epsilon}\}\subset\mathrm{U}(N)$ in the neighborhood of the critical set $C^{P}\simeq\mathrm{U}(\mathbf{n})P\mathrm{U}(\mathbf{m})$ of the kinematic quantum ensemble control landscape J(U) = Tr(U\rho U' O), where $U$ represents the unitary time evolution operator, {\rho} is the initial density matrix of the ensemble, and O is an observable operator. This estimate is based on the Hilbert-Schmidt geometry for the unitary group and a first-order approximation of $||grad J(U)||^2$. An upper bound on these near-critical volumes is conjectured and supported by numerical simulation, leading to an asymptotic analysis as the dimension $N$ of the quantum system rises in which the volume fractions of these "near-critical" sets decrease to zero as $N$ increases. This result helps explain the apparent lack of influence exerted by the many saddles of $J$ over the gradient flow.Comment: 27 pages, 1 figur

The activation energy for GaAs/AlGaAs interdiffusion

Copyright 1997 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. This article appeared in Journal of Applied Physics 82, 4842 (1997) and may be found at