Energy Localization in the Peyrard-Bishop DNA model

We study energy localization on the oscillator-chain proposed by Peyrard and Bishop to model the DNA. We search numerically for conditions with initial energy in a small subgroup of consecutive oscillators of a finite chain and such that the oscillation amplitude is small outside this subgroup for a long timescale. We use a localization criterion based on the information entropy and we verify numerically that such localized excitations exist when the nonlinear dynamics of the subgroup oscillates with a frequency inside the reactive band of the linear chain. We predict a mimium value for the Morse parameter $(\mu >2.25)$ (the only parameter of our normalized model), in agreement with the numerical calculations (an estimate for the biological value is $\mu =6.3$). For supercritical masses, we use canonical perturbation theory to expand the frequencies of the subgroup and we calculate an energy threshold in agreement with the numerical calculations

Bubble generation in a twisted and bent DNA-like model

The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally distributed initial conditions to simulate thermal fluctuations, a relationship between bubble generation, twist and curvature is established. An analytical approach supports the numerical results.Comment: 7 pages, 8 figures. Accepted for Phys. Rev. E (in press

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

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Revised design guidelines and specifications for Apollo telescope mount control and display consol

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

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

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

Attraction between DNA molecules mediated by multivalent ions

The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counter- and salt ions and different salt concentrations. Computer simulations of the primitive model are used and the shape of the DNA molecules is accurately modelled using different geometrical shapes. We find that multivalent ions induce a significant attraction between the DNA molecules whose strength can be tuned by the averaged valency of the ions. The physical origin of the attraction is traced back either to electrostatics or to entropic contributions. For multivalent counter- and monovalent salt ions, we find a salt-induced stabilization effect: the force is first attractive but gets repulsive for increasing salt concentration. Furthermore, we show that the multivalent-ion-induced attraction does not necessarily correlate with DNA overcharging.Comment: 51 pages and 13 figure