Slow compressional wave in porous media: Finite difference simulations on micro-scale

We perform wave propagation simulations in porous media on microscale in which a slow compressional wave can be observed. Since the theory of dynamic poroelasticity was developed by Biot (1956), the existence of the type II or Biot's slow compressional wave (SCW) remains the most controversial of its predictions. However, this prediction was confirmed experimentally in ultrasonic experiments. The purpose of this paper is to observe the SCW by applying a recently developed viscoelastic displacement-stress rotated staggered finite-difference (FD) grid technique to solve the elastodynamic wave equation. To our knowledge this is the first time that the slow compressional wave is simulated on first principles

Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit expands an accompanying overview unit (UNIT ) by discussing methods used to treat the energy and sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143698/1/cpnc0708.pd

Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Effect of shear force on the separation of double stranded DNA

Using the Langevin Dynamics simulation, we have studied the effects of the shear force on the rupture of short double stranded DNA at different temperatures. We show that the rupture force increases linearly with the chain length and approaches to the asymptotic value in accordance with the experiment. The qualitative nature of these curves almost remains same for different temperatures but with a shift in the force. We observe three different regimes in the extension of covalent bonds (back bone) under the shear force.Comment: 4 pages, 4 figure

Effects of finite curvature on soliton dynamics in a chain of nonlinear oscillators

We consider a curved chain of nonlinear oscillators and show that the interplay of curvature and nonlinearity leads to a number of qualitative effects. In particular, the energy of nonlinear localized excitations centered on the bending decreases when curvature increases, i.e. bending manifests itself as a trap for excitations. Moreover, the potential of this trap is double-well, thus leading to a symmetry breaking phenomenon: a symmetric stationary state may become unstable and transform into an energetically favorable asymmetric stationary state. The essentials of symmetry breaking are examined analytically for a simplified model. We also demonstrate a threshold character of the scattering process, i.e. transmission, trapping, or reflection of the moving nonlinear excitation passing through the bending.Comment: 13 pages (LaTeX) with 10 figures (EPS

Competition for hydrogen bond formation in the helix-coil transition and protein folding

The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure; and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.Comment: 21 pages, 3 figures, submitted to Phys Rev

Reversible Metal-Semiconductor Transition of ssDNA-Decorated Single-Walled Carbon Nanotubes

A field effect transistor (FET) measurement of a SWNT shows a transition from a metallic one to a p-type semiconductor after helical wrapping of DNA. Water is found to be critical to activate this metal-semiconductor transition in the SWNT-ssDNA hybrid. Raman spectroscopy confirms the same change in electrical behavior. According to our ab initio calculations, a band gap can open up in a metallic SWNT with wrapped ssDNA in the presence of water molecules due to charge transfer.Comment: 13 pages, 6 figure

Comparison of urinary 6‐β‐cortisol and the erythromycin breath test as measures of hepatic P450IIIA (CYP3A) activity

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110077/1/cptclpt1992140.pd

Analytical considerations in deriving 99th percentile upper reference limits for high-sensitivity cardiac troponin assays: Educational recommendations from the IFCC committee on clinical application of cardiac bio-markers

The International Federation of Clinical Chemistry Committee on Clinical Application of Cardiac Bio-Markers provides evidence-based educational documents to facilitate uniform interpretation and utilization of cardiac biomarkers in clinical laboratories and practice. The committee’s goals are to improve the understanding of certain key analytical and clinical aspects of cardiac biomarkers and how these may interplay in clinical practice. Measurement of high-sensitivity cardiac troponin (hs-cTn) assays is a cornerstone in the clinical evaluation of patients with symptoms and/or signs of acute cardiac ischemia. To define myocardial infarction, the Universal Definition of Myocardial Infarction requires patients who manifest with features suggestive of acute myocardial ischemia to have at least one cTn concentration above the sex-specific 99th percentile upper reference limit (URL) for hs-cTn assays and a dynamic pattern of cTn concentrations to fulfill the diagnostic criteria for MI. This special report provides an overview of how hs-cTn 99th percentile URLs should be established, including recommendations about prescreening and the number of individuals required in the reference cohort, how statistical analysis should be conducted, optimal preanalytical and analytical protocols, and analytical/biological interferences or confounds that can affect accurate determination of the 99th percentile URLs. This document also provides guidance and solutions to many of the issues posed.publishedVersio

Numerical Calculations of the B1g Raman Spectrum of the Two-Dimensional Heisenberg Model

The B1g Raman spectrum of the two-dimensional S=1/2 Heisenberg model is discussed within Loudon-Fleury theory at both zero and finite temperature. The exact T=0 spectrum for lattices with up to 6*6 sites is computed using Lanczos exact diagonalization. A quantum Monte Carlo (QMC) method is used to calculate the corresponding imaginary-time correlation function and its first two derivatives for lattices with up to 16*16 spins. The imaginary-time data is continued to real frequency using the maximum-entropy method, as well as a fit based on spinwave theory. The numerical results are compared with spinwave calculations for finite lattices. There is a surprisingly large change in the exact spectrum going from 4*4 to 6*6 sites. In the former case there is a single dominant two-magnon peak at frequency w/J appr. 3.0, whereas in the latter case there are two approximately equal-sized peaks at w/J appr. 2.7 and 3.9. This is in good qualitative agreement with the spinwave calculations including two-magnon processes on the same lattices. Both the Lanczos and the QMC results indicate that the actual infinite-size two-magnon profile is broader than the narrow peak obtained in spinwave theory, but the positions of the maxima agree to within a few percent. The higher-order contributions present in the numerical results are merged with the two-magnon profile and extend up to frequencies w/J appr. 7. The first three frequency cumulants of the spectrum are in excellent agreement with results previously obtained from a series expansion around the Ising limit. Typical experimental B1g$ spectra for La2CuO4 are only slightly broader than what we obtain here. The exchange constant extracted from the peak position is J appr. 1400K, in good agreement with values obtained from neutron scattering and NMR experiments.Comment: 15 pages, Revtex, 13 PostScript figure