Inhibition of DNA ejection from bacteriophage by Mg+2 counterions

The problem of inhibiting viral DNA ejection from bacteriophages by multivalent counterions, specifically Mg$^{+2}$ counterions, is studied. Experimentally, it is known that MgSO$_4$ salt has a strong and non-monotonic effect on the amount of DNA ejected. There exists an optimal concentration at which the minimum amount of DNA is ejected from the virus. At lower or higher concentrations, more DNA is ejected from the capsid. We propose that this phenomenon is the result of DNA overcharging by Mg$^{+2}$ multivalent counterions. As Mg$^{+2}$ concentration increases from zero, the net charge of DNA changes from negative to positive. The optimal inhibition corresponds to the Mg$^{+2}$ concentration where DNA is neutral. At lower/higher concentrations, DNA genome is charged. It prefers to be in solution to lower its electrostatic self-energy, which consequently leads to an increase in DNA ejection. By fitting our theory to available experimental data, the strength of DNA$-$DNA short range attraction energies, mediated by Mg$^{+2}$, is found to be $-$0.004 $k_BT$ per nucleotide base. This and other fitted parameters agree well with known values from other experiments and computer simulations. The parameters are also in aggreement qualitatively with values for tri- and tetra-valent counterions.Comment: 17 pages, 4 figures, improved manuscript. Submitted to J. Chem. Phys (2010

Effects of translational and rotational degrees of freedom on the properties of model water

Molecular dynamics simulations with separate thermostats for rotational and translational motions were used to study the effects of these degrees of freedom on the structure of water at a fixed density. To describe water molecules, we used the SPC/E model. The results indicate that an increase of the rotational temperature, $T_\textrm{R}$, causes a significant breaking of the hydrogen bonds. This is not the case, at least not to such an extent, when the translational temperature, $T_\textrm{T}$, is raised. The probability of finding an empty spherical cavity (no water molecule present) of a given size, strongly decreases with an increase of $T_\textrm{R}$, but this only marginally affects the free energy of the hydrophobe insertion. The excess internal energy increases proportionally with an increase of $T_\textrm{R}$, while an increase of $T_\textrm{T}$ yields a much smaller effect at high temperatures. The diffusion coefficient of water exhibits a non-monotonous behaviour with an increase of the rotational temperature.Comment: 9 pages, 9 figure

Double charmonium production at B-factories within light cone formalism

This paper is devoted to the study of the processes e^+e^- \to J/\Psi \eta_c, J/\Psi \eta_c', \psi' \eta_c, \psi' \eta_c' within light cone formalism. It is shown that if one disregards the contribution of higher fock states, the twist-3 distribution amplitudes needed in the calculation can be unambiguously determined from the twist-2 distribution amplitudes and equations of motion. Using models of the twist-2 distribution amplitudes the cross sections of the processes under study have been calculated. The results of the calculation are in agreement with Belle and BaBar experiments. It is also shown that relativistic and radiative corrections to the cross sections play crucial role in the achievement of the agreement between the theory and experiments. The comparison of the results of this paper with the results obtained in other papers has been carried out. In particular, it is shown that the results of papers where relativistic and radiative corrections were calculated within NRQCD are overestimated by a factor of ~1.5.Comment: 14 pages, 1 figur

Quasi-dark Mode in a Metamaterial for Analogous Electromagnetically-induced Transparency

We study a planar metamaterial supporting electromagnetically-induced transparency (EIT)-like effect by exploiting the coupling between bright and quasi-dark eigenmodes. The specific design of such a metamaterial consists of a cut-wire (CW) and a single-gap split-ring resonator (SRR). From the numerical and the analytical results we demonstrate that the response of SRR, which is weakly excited by external electric field, is mitigated to be a quasi-dark eigenmode in the presence of strongly radiative CW. This result suggests more relaxed conditions for the realization of devices utilizing the EIT-like effects in metamaterial, and thereby widens the possibilities for many different structural implementations.Comment: 11 pages, 4 figure

Fluorine in a Carbon-Enhanced Metal-Poor Star

The fluorine abundance of the Carbon-Enhanced Metal-Poor (CEMP) star HE 1305+0132 has been derived by analysis of the molecular HF (1-0) R9 line at 2.3357 microns in a high-resolution (R = 50,000) spectrum obtained with the Phoenix spectrometer and Gemini-South telescope. Our abundance analysis makes use of a CNO-enhanced ATLAS12 model atmosphere characterized by a metallicity and CNO enhancements determined utilizing medium-resolution (R = 3,000) optical and near-IR spectra. The effective iron abundance is found to be [Fe/H] = -2.5, making HE 1305+0132 the most Fe-deficient star, by more than an order of magnitude, for which the abundance of fluorine has been measured. Using spectral synthesis, we derive a super-solar fluorine abundance of A(19F) = 4.96 +/- 0.21, corresponding to a relative abundance of [F/Fe] = 2.90. A single line of the Phillips C_2 system is identified in our Phoenix spectrum, and along with multiple lines of the first-overtone vibration-rotation CO (3-1) band head, C and O abundances of A(12C) = 8.57 +/- 0.11 and A(16O) = 7.04 +/- 0.14 are derived. We consider the striking fluorine overabundance in the framework of the nucleosynthetic processes thought to be responsible for the C-enhancement of CEMP stars and conclude that the atmosphere of HE 1305+0132 was polluted via mass transfer by a primary companion during its asymptotic giant branch phase. This is the first study of fluorine in a CEMP star, and it demonstrates that this rare nuclide can be a key diagnostic of nucleosynthetic processes in the early Galaxy.Comment: 13 pages, 3 figures; Accepted for publication in ApJ Letter

Vibrational state dependence of ionic rotational branching ratios in resonance enhanced multiphoton ionization of CH

We show that rapid evolution of a Rydberg orbital with internuclear distance in a resonance enhanced multiphoton ionization (REMPI) process can have a profound influence on the production of molecular ions in alternative rotational states. This is illustrated by calculations of ionic rotational branching ratios for (2+1′) REMPI via the O11 (20.5) branch of the E′ ^2Σ^+(3pσ) Rydberg state of CH. The rotational propensity rule for ionization changes from ΔN=odd (ΔN=N_+−N_i) at lower vibrational excitation, as expected from the ΔN+l=odd selection rule, to ΔN=even at higher vibrational levels. This effect is expected to be quite general and should be most readily observable in diatomic hydrides

Three-Species Diffusion-Limited Reaction with Continuous Density-Decay Exponents

We introduce a model of three-species two-particle diffusion-limited reactions A+B -> A or B, B+C -> B or C, and C+A -> C or A, with three persistence parameters (survival probabilities in reaction) of the hopping particle. We consider isotropic and anisotropic diffusion (hopping with a drift) in 1d. We find that the particle density decays as a power-law for certain choices of the persistence parameter values. In the anisotropic case, on one symmetric line in the parameter space, the decay exponent is monotonically varying between the values close to 1/3 and 1/2. On another, less symmetric line, the exponent is constant. For most parameter values, the density does not follow a power-law. We also calculated various characteristic exponents for the distance of nearest particles and domain structure. Our results support the recently proposed possibility that 1d diffusion-limited reactions with a drift do not fall within a limited number of distinct universality classes.Comment: 12 pages in plain LaTeX and four Postscript files with figure