Opening of DNA double strands by helicases. Active versus passive opening

Helicase opening of double-stranded nucleic acids may be "active" (the helicase directly destabilizes the dsNA to promote opening) or "passive" (the helicase binds ssNA available due to a thermal fluctuation which opens part of the dsNA). We describe helicase opening of dsNA, based on helicases which bind single NA strands and move towards the double-stranded region, using a discrete ``hopping'' model. The interaction between the helicase and the junction where the double strand opens is characterized by an interaction potential. The form of the potential determines whether the opening is active or passive. We calculate the rate of passive opening for the helicase PcrA, and show that the rate increases when the opening is active. Finally, we examine how to choose the interaction potential to optimize the rate of strand separation. One important result is our finding that active opening can increase the unwinding rate by 7 fold compared to passive opening.Comment: 13 pages, 3 figure

Determination of Ethanol Content in Fuels with Phononic Crystal Sensor

Introduction. In-line analysis of ethanol content in gasoline blends is currently one of the urgent needs of fuel industry. Developing safe and secure approaches is critical for real applications. A phononic crystal sensor have been introduced as an innovative approach to high performance gasoline sensing. Distinguishing feature of proposed sensor is the absence of any electrical contact with analysed gasoline blend, which allows the use of sensors directly in pipelines without the risk of explosion in an emergency.Aim. Investigation of the possibilities of using phononic sensor structures to determine the ethanol content in liquid hydrocarbons.Materials and methods. A theoretical analysis of sensor structure was carried out on the basis of numerical simulation using COMSOL Multiphysics software. For measurement, substances of ordinary gasoline and gasoline 63–80 with ethanol concentrations in the range of 1–10 % by volume in increments of 2 % were prepared. The phononic crystal sensor was designed as a stainless steel plate with cylindrical holes and a resonant cavity, formed as a running across the wave propagation path slit between two lattices.Results. In-line analysis of measuring the concentration of ethanol in alcohol-containing fuels on a phononic crystal structure with a resonant cavity was carried out. Using the Agilent4395A admittance meter, the transmission spectra of longitudinal acoustic waves through the gasoline-filled sensor structure with were obtained. The non-linear correlation between the composition and the speed of sound of the blend is presented in the article is due to the ability to reduce the speed of sound of the mixture with an increase in ethanol concentration in the range of 0–10 % by volume.Conclusion. A measurement structure on the basis of phononic crystal was created. The measurements of various gasoline-ethanol mixtures show that the sensor has significant sensitivity (0.91 kHz/ms−1 ) with quality factor of 200) to distinguish between regular fuels, gasoline based blends and the presence of additives in standard fuels. The sensor has prospects for in-line analyzes the composition of liquid hydrocarbons.Introduction. In-line analysis of ethanol content in gasoline blends is currently one of the urgent needs of fuel industry. Developing safe and secure approaches is critical for real applications. A phononic crystal sensor have been introduced as an innovative approach to high performance gasoline sensing. Distinguishing feature of proposed sensor is the absence of any electrical contact with analysed gasoline blend, which allows the use of sensors directly in pipelines without the risk of explosion in an emergency.Aim. Investigation of the possibilities of using phononic sensor structures to determine the ethanol content in liquid hydrocarbons.Materials and methods. A theoretical analysis of sensor structure was carried out on the basis of numerical simulation using COMSOL Multiphysics software. For measurement, substances of ordinary gasoline and gasoline 63–80 with ethanol concentrations in the range of 1–10 % by volume in increments of 2 % were prepared. The phononic crystal sensor was designed as a stainless steel plate with cylindrical holes and a resonant cavity, formed as a running across the wave propagation path slit between two lattices.Results. In-line analysis of measuring the concentration of ethanol in alcohol-containing fuels on a phononic crystal structure with a resonant cavity was carried out. Using the Agilent4395A admittance meter, the transmission spectra of longitudinal acoustic waves through the gasoline-filled sensor structure with were obtained. The non-linear correlation between the composition and the speed of sound of the blend is presented in the article is due to the ability to reduce the speed of sound of the mixture with an increase in ethanol concentration in the range of 0–10 % by volume.Conclusion. A measurement structure on the basis of phononic crystal was created. The measurements of various gasoline-ethanol mixtures show that the sensor has significant sensitivity (0.91 kHz/ms−1 ) with quality factor of 200) to distinguish between regular fuels, gasoline based blends and the presence of additives in standard fuels. The sensor has prospects for in-line analyzes the composition of liquid hydrocarbons

Effects of the current financial and economic crisis on the rural landscape as well as the agri-food sector in Europe and Central Asia

This paper reviews the expected effects of the current financial crisis and subsequent recession on the rural landscape, in particular the agri-food sector in Europe and Central Asia (ECA) on the basis of the structure of the rural economy and of different organisations and institutions. Empirical evidence suggests that the crisis has hit the ECA region the hardest. Agriculture contributes about 9% to gross domestic product (GDP) for the ECA region as a whole with 16% of the population being employed in the agricultural sector. As far as the impact of the financial crisis on the agri-food sector is concerned, there are a few interconnected issues: (1) reduction in income elastic food demand and commodity price decline, (2) loss of employment and earnings of rural people working in urban centres, implying also costly labour reallocation, (3) rising rural poverty originating mainly from lack of opportunities in the non-farm sector and a sizable decline of international remittances, (4) tightening of agricultural credit markets, and the (5) collapse of sectoral government support programs and social safety-net measures in many countries. The paper reveals how the crisis hit farming and broader agri-business differently in general and in the ECA sub-regions

Design of deeply cooled ultra-low dissipation amplifier and measuring cell for quantum measurements with a microwave single-photon counter

The requirements and details of designing a measuring cell and low-back-action deeply-cooled amplifier for quantum measurements at 10 mK are discussed. This equipment is a part of a microwave single-photon counter based on a superconducting flux qubit. The high electron mobility transistors (HEMTs) in the amplifier operate in unsaturated microcurrent regime and dissipate only 1 microwatt of dc power per transistor. Simulated amplifier gain is 15 dB at 450 MHz with a high-impedance (~5 kOhm signal source and standard 50-Ohm output.Comment: 10 pages, 7 figures. To be published in Fizika Nizkikh Temperatur (Low Temperature Physics) vol. 50, No.1 (2024

An improvement of the Berry--Esseen inequality with applications to Poisson and mixed Poisson random sums

By a modification of the method that was applied in (Korolev and Shevtsova, 2009), here the inequalities $$\rho(F_n,\Phi)\le\frac{0.335789(\beta^3+0.425)}{\sqrt{n}}$$ and $$\rho(F_n,\Phi)\le \frac{0.3051(\beta^3+1)}{\sqrt{n}}$$ are proved for the uniform distance $\rho(F_n,\Phi)$ between the standard normal distribution function $\Phi$ and the distribution function $F_n$ of the normalized sum of an arbitrary number $n\ge1$ of independent identically distributed random variables with zero mean, unit variance and finite third absolute moment $\beta^3$. The first of these inequalities sharpens the best known version of the classical Berry--Esseen inequality since $0.335789(\beta^3+0.425)\le0.335789(1+0.425)\beta^3<0.4785\beta^3$ by virtue of the condition $\beta^3\ge1$, and 0.4785 is the best known upper estimate of the absolute constant in the classical Berry--Esseen inequality. The second inequality is applied to lowering the upper estimate of the absolute constant in the analog of the Berry--Esseen inequality for Poisson random sums to 0.3051 which is strictly less than the least possible value of the absolute constant in the classical Berry--Esseen inequality. As a corollary, the estimates of the rate of convergence in limit theorems for compound mixed Poisson distributions are refined.Comment: 33 page

Hydrogen Molecules In Superstrong Magnetic Field: II. Excitation Levels

We study the energy levels of H$_2$ molecules in a superstrong magnetic field (B\go 10^{12} G), typically found on the surfaces of neutron stars. The interatomic interaction potentials are calculated by a Hartree-Fock method with multi-configurations assuming electrons are in the ground Landau state. Both the aligned configurations and arbitrary orientations of the molecular axis with respect to the magnetic field axis are considered. Different types of molecular excitations are then studied: electronic excitations, aligned (along the magnetic axis) vibrational excitations, transverse vibrational excitations (a constrained rotation of the molecular axis around the magnetic field line). Similar results for the molecular ion H$_2^+$ are also obtained and compared with previous variational calculations. Both numerical results and analytical fitting formulae are given for a wide range of field strengths. In contrast to the zero-field case, it is found that the transverse vibrational excitation energies can be larger than the aligned vibration excitation, and they both can be comparable or larger than the electronic excitations. For B\go B_{crit}=4.23\times 10^{13} G, the Landau energy of proton is appreciable and there is some controversy regarding the dissociation energy of H$_2$. We show that H$_2$ is bound even for $B>>B_{crit}$ and that neither proton has a Landau excitation in the ground molecular state.Comment: Revtex (45 pages), 3 postscript figures; Phys. Rev. A in pres

Cloud Ice Properties: In Situ Measurement Challenges

Baumgardner D., S.J. Abel, D. Axisa, R. Cotton, J. Crosier, P. Field, C. Gurganus, A. Heymsfield, A. Korolev, M. Krämer, P. Lawson, G. McFarquhar, Z. Ulanowski, and J. Um, 'Cloud ice properties: in situ measurement challenges', Meteorological Monographs, Vol. 58, pp. 9.1–9.23, April 2017. The version of record is available online at doi: 10.1175/AMSMONOGRAPHS-D-16-0011.1.1 © 2017 American Meteorological Society. For information regarding reuse of this content and general copyright information, consult the AMS Copyright Policy (www.ametsoc.org/PUBSReuseLicenses).Understanding the formation and evolution of ice in clouds requires detailed information on the size, shape, mass and optical properties of individual cloud hydrometeors and their bulk properties over a broad range of atmospheric conditions. Since the 1960s, instrumentation and research aircraft have evolved providing increasingly more accurate and larger quantities of data about cloud particle properties. In this chapter we review the current status of electrical powered, in situ measurement systems with respect to their strengths and weaknesses and document their limitations and uncertainties. There remain many outstanding challenges. These are summarized and accompanied by recommendations for moving forward. through new developments that fill the remaining information gaps. Closing these gaps will remove the obstacles that continue to hinder our understanding of cloud processes in general and the evolution of ice in particular.Peer reviewe

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