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

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

Multi-site breathers in Klein-Gordon lattices: stability, resonances, and bifurcations

We prove the most general theorem about spectral stability of multi-site breathers in the discrete Klein-Gordon equation with a small coupling constant. In the anti-continuum limit, multi-site breathers represent excited oscillations at different sites of the lattice separated by a number of "holes" (sites at rest). The theorem describes how the stability or instability of a multi-site breather depends on the phase difference and distance between the excited oscillators. Previously, only multi-site breathers with adjacent excited sites were considered within the first-order perturbation theory. We show that the stability of multi-site breathers with one-site holes change for large-amplitude oscillations in soft nonlinear potentials. We also discover and study a symmetry-breaking (pitchfork) bifurcation of one-site and multi-site breathers in soft quartic potentials near the points of 1:3 resonance.Comment: 34 pages, 12 figure

Kramers-Kronig constrained variational analysis of optical spectra

A universal method of extraction of the complex dielectric function $\epsilon(\omega)=\epsilon_{1}(\omega)+i\epsilon_{2}(\omega)$ from experimentally accessible optical quantities is developed. The central idea is that $\epsilon_{2}(\omega)$ is parameterized independently at each node of a properly chosen anchor frequency mesh, while $\epsilon_{1}(\omega)$ is dynamically coupled to $\epsilon_{2}(\omega)$ by the Kramers-Kronig (KK) transformation. This approach can be regarded as a limiting case of the multi-oscillator fitting of spectra, when the number of oscillators is of the order of the number of experimental points. In the case of the normal-incidence reflectivity from a semi-infinite isotropic sample the new method gives essentially the same result as the conventional KK transformation of reflectivity. In contrast to the conventional approaches, the proposed technique is applicable, without readaptation, to virtually all types of linear-response optical measurements, or arbitrary combinations of measurements, such as reflectivity, transmission, ellipsometry {\it etc.}, done on different types of samples, including thin films and anisotropic crystals.Comment: 10 pages, 7 figure

An efficient algorithm for computing the Baker-Campbell-Hausdorff series and some of its applications

We provide a new algorithm for generating the Baker--Campbell--Hausdorff (BCH) series Z = \log(\e^X \e^Y) in an arbitrary generalized Hall basis of the free Lie algebra $\mathcal{L}(X,Y)$ generated by $X$ and $Y$. It is based on the close relationship of $\mathcal{L}(X,Y)$ with a Lie algebraic structure of labeled rooted trees. With this algorithm, the computation of the BCH series up to degree 20 (111013 independent elements in $\mathcal{L}(X,Y)$) takes less than 15 minutes on a personal computer and requires 1.5 GBytes of memory. We also address the issue of the convergence of the series, providing an optimal convergence domain when $X$ and $Y$ are real or complex matrices.Comment: 30 page

Scar functions in the Bunimovich Stadium billiard

In the context of the semiclassical theory of short periodic orbits, scar functions play a crucial role. These wavefunctions live in the neighbourhood of the trajectories, resembling the hyperbolic structure of the phase space in their immediate vicinity. This property makes them extremely suitable for investigating chaotic eigenfunctions. On the other hand, for all practical purposes reductions to Poincare sections become essential. Here we give a detailed explanation of resonances and scar functions construction in the Bunimovich stadium billiard and the corresponding reduction to the boundary. Moreover, we develop a method that takes into account the departure of the unstable and stable manifolds from the linear regime. This new feature extends the validity of the expressions.Comment: 21 pages, 10 figure

Phase Splitting for Periodic Lie Systems

In the context of the Floquet theory, using a variation of parameter argument, we show that the logarithm of the monodromy of a real periodic Lie system with appropriate properties admits a splitting into two parts, called dynamic and geometric phases. The dynamic phase is intrinsic and linked to the Hamiltonian of a periodic linear Euler system on the co-algebra. The geometric phase is represented as a surface integral of the symplectic form of a co-adjoint orbit.Comment: (v1) 15 pages. (v2) 16 pages. Some typos corrected. References and further comments added. Final version to appear in J. Phys. A

Molecular dynamics study of accelerated ion-induced shock waves in biological media

We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and equilibrate DNA duplexes in liquid water boxes of different sizes and shapes. The translational and vibrational degrees of freedom of water molecules are excited according to the energy deposited by the ions and the subsequent shock waves in liquid water are simulated. The pressure waves generated are studied and compared with an analytical hydrodynamics model which serves as a benchmark for evaluating the suitability of the simulation boxes. The energy deposition in the DNA backbone bonds is also monitored as an estimation of biological damage, something which is not possible with the analytical model