Multiscale approach to radiation damage induced by ion beams: complex DNA damage and effects of thermal spikes

We present the latest advances of the multiscale approach to radiation damage caused by irradiation of a tissue with energetic ions and report the most recent advances in the calculations of complex DNA damage and the effects of thermal spikes on biomolecules. The multiscale approach aims to quantify the most important physical, chemical, and biological phenomena taking place during and following irradiation with ions and provide a better means for clinically-necessary calculations with adequate accuracy. We suggest a way of quantifying the complex clustered damage, one of the most important features of the radiation damage caused by ions. This method can be used for the calculation of irreparable DNA damage. We include thermal spikes, predicted to occur in tissue for a short time after ion's passage in the vicinity of the ions' tracks in our previous work, into modeling of the thermal environment for molecular dynamics analysis of ubiquitin and discuss the first results of these simulations.Comment: 14 pages, 3 figures, submitted to EPJ

On the variance of the number of occupied boxes

We consider the occupancy problem where balls are thrown independently at infinitely many boxes with fixed positive frequencies. It is well known that the random number of boxes occupied by the first n balls is asymptotically normal if its variance V_n tends to infinity. In this work, we mainly focus on the opposite case where V_n is bounded, and derive a simple necessary and sufficient condition for convergence of V_n to a finite limit, thus settling a long-standing question raised by Karlin in the seminal paper of 1967. One striking consequence of our result is that the possible limit may only be a positive integer number. Some new conditions for other types of behavior of the variance, like boundedness or convergence to infinity, are also obtained. The proofs are based on the poissonization techniques.Comment: 34 page

Alpha helix-coil phase transition: analysis of ab initio theory predictions

In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of different length. We have calculated the potential energy surfaces of polypeptides with respect to their twisting degrees of freedom and construct a parameter-free partition function of the polypeptide using the suggested method [1]. From the build up partition function we derive various thermodynamical characteristics for alanine polypeptides of different length as a function of temperature. Thus, we analyze the temperature dependence of the heat capacity, latent heat and helicity for alanine polypeptides consisting of 21, 30, 40, 50 and 100 amino acids. Alternatively, we have obtained same thermodynamical characteristics from the use of molecular dynamics simulations and compared them with the results of the new statistical mechanics approach. The comparison proves the validity of the statistical mechanic approach and establishes its accuracy.Comment: 34 pages, 12 figure

Elliptic instability in the Lagrangian-averaged Euler-Boussinesq-alpha equations

We examine the effects of turbulence on elliptic instability of rotating stratified incompressible flows, in the context of the Lagragian-averaged Euler-Boussinesq-alpha, or \laeba, model of turbulence. We find that the \laeba model alters the instability in a variety of ways for fixed Rossby number and Brunt-V\"ais\"al\"a frequency. First, it alters the location of the instability domains in the $(\gamma,\cos\theta)-$parameter plane, where $\theta$ is the angle of incidence the Kelvin wave makes with the axis of rotation and $\gamma$ is the eccentricity of the elliptic flow, as well as the size of the associated Lyapunov exponent. Second, the model shrinks the width of one instability band while simultaneously increasing another. Third, the model introduces bands of unstable eccentric flows when the Kelvin wave is two-dimensional. We introduce two similarity variables--one is a ratio of the Brunt-V\"ais\"al\"a frequency to the model parameter $\Upsilon_0 = 1+\alpha^2\beta^2$, and the other is the ratio of the adjusted inverse Rossby number to the same model parameter. Here, $\alpha$ is the turbulence correlation length, and $\beta$ is the Kelvin wave number. We show that by adjusting the Rossby number and Brunt-V\"ais\"al\"a frequency so that the similarity variables remain constant for a given value of $\Upsilon_0$, turbulence has little effect on elliptic instability for small eccentricities $(\gamma \ll 1)$. For moderate and large eccentricities, however, we see drastic changes of the unstable Arnold tongues due to the \laeba model.Comment: 23 pages (sigle spaced w/figure at the end), 9 figures--coarse quality, accepted by Phys. Fluid

Ab initio theory of helix-coil phase transition

In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).Comment: 24 pages, 3 figure

Suboptimal quantum-error-correcting procedure based on semidefinite programming

In this paper, we consider a simplified error-correcting problem: for a fixed encoding process, to find a cascade connected quantum channel such that the worst fidelity between the input and the output becomes maximum. With the use of the one-to-one parametrization of quantum channels, a procedure finding a suboptimal error-correcting channel based on a semidefinite programming is proposed. The effectiveness of our method is verified by an example of the bit-flip channel decoding.Comment: 6 pages, no figure, Some notations differ from those in the PRA versio

Rigorous derivation of coherent resonant tunneling time and velocity in finite periodic systems

The velocity $v_{res}$ of resonant tunneling electrons in finite periodic structures is analytically calculated in two ways. The first method is based on the fact that a transmission of unity leads to a coincidence of all still competing tunneling time definitions. Thus, having an indisputable resonant tunneling time $\tau_{res},$ we apply the natural definition $v_{res}=L/\tau_{res}$ to calculate the velocity. For the second method we combine Bloch's theorem with the transfer matrix approach to decompose the wave function into two Bloch waves. Then the expectation value of the velocity is calculated. Both different approaches lead to the same result, showing their physical equivalence. The obtained resonant tunneling velocity $v_{res}$ is smaller or equal to the group velocity times the magnitude of the complex transmission amplitude of the unit cell. Only at energies where the unit cell of the periodic structure has a transmission of unity $v_{res}$ equals the group velocity. Numerical calculations for a GaAs/AlGaAs superlattice are performed. For typical parameters the resonant velocity is below one third of the group velocity.Comment: 12 pages, 3 figures, LaTe

A forecast model for a road network’s section traffic capacity assessment on a territory of the cryolithozone in conditions of the climate change

A model is proposed in which the capacity of the road network section depends on the technical and operational condition of the road surface – the presence of sinkholes, potholes, ruts, as well as their predictive depth. Appearing of these defects on the road surface is associated with excessive thawing and permafrost soil settlement in the formation occurring under the influence of the climate change. The soil thawing depth is modelled on the basis of predictive climatic parameters during the full average year, and then the maximum thawing depth and the corresponding soil settlement is determined. Three main scenarios of the climate change are considered: temperature contrast increasing, uniform warming and their combination. The assumed value of warming or temperature contrast increasing is considered to be a random value distributed according to the normal law; the predicted decrease in the road section capacity is defined as a weighted average over the entire range of possible climate changes. According to the results of the numerical implementation of the model on the road network sections for natural and climatic conditions of Yakutia, it is shown that in the third scenario of the climate change the road network section capacity is predicted to decrease from 17% (the formation is dry sandy permafrost soil) to 50% (the formation is clay soil of high humidity). The impact of natural and climatic features of the territory is predicted to be at a level up to 10% of the total reduction in the capacity of road network sections