Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics

The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the $\phi$X174 phage without any adjustable parameters are in good agreement with experiment. The calculated probabilities for single base-pair opening are consistent with values obtained from imino proton exchange experiments.Comment: 5 pages, 4 figures, to appear in Phys. Rev.

Acceleration and transport of ions in turbulent current sheets: formation of non-maxwelian energy distribution

The paper is devoted to particle acceleration in turbulent current sheet (CS). Our results show that the mechanism of CS particle interaction with electromagnetic turbulence can explain the formation of power law energy distributions. We study the ratio between adiabatic acceleration of particles in electric field in the presence of stationary turbulence and acceleration due to electric field in the case of dynamic turbulence. The correlation between average energy gained by particles and average particle residence time in the vicinity of the neutral sheet is discussed. It is also demonstrated that particle velocity distributions formed by particle-turbulence interaction are similar in essence to the ones observed near the far reconnection region in the Earth's magnetotail

Denaturation transition of stretched DNA

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase diagram. The transition is determined by the loop exponent $c$ for which we find the new value $c=4\nu-1/2$ such that the transition is second order with $c=1.85<2$ in $d=3$. We show that a finite stretching force $F$ destabilizes DNA, corresponding to a lower melting temperature $T(F)$, in agreement with single-molecule DNA stretching experiments.Comment: 5 pages, 3 figure

Dispersion-theoretical analysis of the nucleon electromagnetic form factors: Inclusion of time-like data

We update a recent dispersion--theoretical fit to the nucleon electromagnetic form factors by including the existing data in the time--like region. We show that while the time--like data for the proton can be described consistently with the existing world space--like data, this is not the case for the neutron. Another measurement of the process $e^+ e^- \to \bar n n$ is called for. We furthermore sharpen the previous estimate of the separation between the perturbative and the non--perturbative regime, which is characterized by a scale parameter $\Lambda^2 \simeq 10\,$GeV$^2$.Comment: 7 pp, LaTeX, uses epsf, 2 figures in separate file, four data points changed, slight changes in the fits, conclusions unchange

Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical Physics (ed. G. Gaeta

Ion kinetic properties in Mercury's pre-midnight plasma sheet

With data from the Fast Imaging Plasma Spectrometer sensor on the MErcury Surface, Space ENvironment, GEochemistry, and Ranging spacecraft, we demonstrate that the average distributions for both solar wind and planetary ions in Mercury’s pre-midnight plasma sheet are well-described by hot Maxwell-Boltzmann distributions. Temperatures and densities of the H+ ranges ~1–10 cm3 and ~5–30 MK, respectively, maintain thermal pressures of ~1 nPa. The dominant planetary ion, Na+ abundances with respect to H+ and exhibit mass-proportional ion temperatures, indicative of a reconnection-dominated heating in the magnetosphere. Conversely, planetary ion species are accelerated to similar average energies greater by a factor of ~1.5 than that of H+ acceleration in an electric potential, consistent with the presence of a strong centrifugal acceleration process in Mercury’s magnetosphere

Kinetic-scale magnetic turbulence and finite Larmor radius effects at Mercury

We use a nonstationary generalization of the higher-order structure function technique to investigate statistical properties of the magnetic field fluctuations recorded by MESSENGER spacecraft during its first flyby (01/14/2008) through the near Mercury's space environment, with the emphasis on key boundary regions participating in the solar wind -- magnetosphere interaction. Our analysis shows, for the first time, that kinetic-scale fluctuations play a significant role in the Mercury's magnetosphere up to the largest resolvable time scale ~20 s imposed by the signal nonstationarity, suggesting that turbulence at this planet is largely controlled by finite Larmor radius effects. In particular, we report the presence of a highly turbulent and extended foreshock system filled with packets of ULF oscillations, broad-band intermittent fluctuations in the magnetosheath, ion-kinetic turbulence in the central plasma sheet of Mercury's magnetotail, and kinetic-scale fluctuations in the inner current sheet encountered at the outbound (dawn-side) magnetopause. Overall, our measurements indicate that the Hermean magnetosphere, as well as the surrounding region, are strongly affected by non-MHD effects introduced by finite sizes of cyclotron orbits of the constituting ion species. Physical mechanisms of these effects and their potentially critical impact on the structure and dynamics of Mercury's magnetic field remain to be understood.Comment: 46 pages, 5 figures, 2 table

A multi-satellite study of accelerated ionospheric ion beams above the polar cap

This paper presents a study of nearly field-aligned outflowing ion beams observed on the Cluster satellites over the polar cap. Data are taken at geocentric radial distances of the order of 5&amp;ndash;9 &lt;i&gt;R&lt;sub&gt;E&lt;/sub&gt;&lt;/i&gt;. The distinction is made between ion beams originating from the polar cusp/cleft and beams accelerated almost along the magnetic field line passing by the spacecraft. Polar cusp beams are characterized by nearly field-aligned proton and oxygen ions with an energy ratio E&lt;sub&gt;O+&lt;/sub&gt; / E&lt;sub&gt;H+&lt;/sub&gt;, of the order of 3 to 4, due to the ion energy repartition inside the source and to the latitudinal extension of the source. Rapid variations in the outflowing ion energy are linked with pulses/modifications of the convection electric field. Cluster data allow one to show that these perturbations of the convection velocity and the associated ion structures propagate at the convection velocity. &lt;P style=&quot;line-height: 20px;&quot;&gt; In contrast, polar cap local ion beams are characterized by field-aligned proton and oxygen ions with similar energies. These beams show the typical inverted V structures usually observed in the auroral zone and are associated with a quasi-static converging electric field indicative of a field-aligned electric field. The field-aligned potential drop fits well the ion energy profile. The simultaneous observation of precipitating electrons and upflowing ions of similar energies at the Cluster orbit indicates that the spacecraft are crossing the mid-altitude part of the acceleration region. In the polar cap, the parallel electric field can thus extend to altitudes higher than 5&amp;nbsp;Earth radii. A detailed analysis of the distribution functions shows that the ions are heated during their parallel acceleration and that energy is exchanged between H&lt;sup&gt;+&lt;/sup&gt; and O&lt;sup&gt;+&lt;/sup&gt;. Furthermore, intense electrostatic waves are observed simultaneously. These observations could be due to an ion-ion two-stream instability

MeV magnetosheath ions energized at the bow shock

A causal relationship between midlatitude magnetosheath energetic ions and bow shock magnetic geometry was previously established for ion energy up to 200 keV e−1 for the May 4, 1998, storm event. This study demonstrates that magnetosheath ions with energies above 200 keV up to 1 MeV simply extend the ion spectrum to form a power law tail. Results of cross-correlation analysis suggest that these ions also come directly from the quasi-parallel bow shock, not the magnetosphere. This is confirmed by a comparison of energetic ion fluxes simultaneously measured in the magnetosheath and at the quasi-parallel bow shock when both regions are likely connected by the magnetic field lines. We suggest that ions are accelerated at the quasi-parallel bow shock to energies as high as 1 MeV and subsequently transported into the magnetosheath during this event