Biodamage via shock waves initiated by irradiation with ions

Radiation damage following the ionising radiation of tissue has different scenarios and mechanisms depending on the projectiles or radiation modality. We investigate the radiation damage effects due to shock waves produced by ions. We analyse the strength of the shock wave capable of directly producing DNA strand breaks and, depending on the ion's linear energy transfer, estimate the radius from the ion's path, within which DNA damage by the shock wave mechanism is dominant. At much smaller values of linear energy transfer, the shock waves turn out to be instrumental in propagating reactive species formed close to the ion's path to large distances, successfully competing with diffusion

Two center multipole expansion method: application to macromolecular systems

We propose a new theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well known fast multipole method. Its efficiency, accuracy and applicability to macromolecular systems is analyzed and discussed in detail.Comment: 23 pages, 7 figures, 1 tabl

Lagrangian Framework for Systems Composed of High-Loss and Lossless Components

Using a Lagrangian mechanics approach, we construct a framework to study the dissipative properties of systems composed of two components one of which is highly lossy and the other is lossless. We have shown in our previous work that for such a composite system the modes split into two distinct classes, high-loss and low-loss, according to their dissipative behavior. A principal result of this paper is that for any such dissipative Lagrangian system, with losses accounted by a Rayleigh dissipative function, a rather universal phenomenon occurs, namely, selective overdamping: The high-loss modes are all overdamped, i.e., non-oscillatory, as are an equal number of low-loss modes, but the rest of the low-loss modes remain oscillatory each with an extremely high quality factor that actually increases as the loss of the lossy component increases. We prove this result using a new time dynamical characterization of overdamping in terms of a virial theorem for dissipative systems and the breaking of an equipartition of energy.Comment: 53 pages, 1 figure; Revision of our original manuscript to incorporate suggestions from refere

Ab initio study of alanine polypeptide chains twisting

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles Phi and Psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.Comment: 24 pages, 10 figure

Crystal structure and spin-trimer magnetism of Rb-2.3(H2O)(0.8)Mn-3[B4P6O24(O,OH)(2)]

The title borophosphate is characterized by a rare combination of the magnetic high-spin Mn2+ ions in both octahedral and tetrahedral coordinations. The crystal structure and magnetic properties are presented.</p

Multi-transmission-line-beam interactive system

We construct here a Lagrangian field formulation for a system consisting of an electron beam interacting with a slow-wave structure modeled by a possibly non-uniform multiple transmission line (MTL). In the case of a single line we recover the linear model of a traveling wave tube (TWT) due to J.R. Pierce. Since a properly chosen MTL can approximate a real waveguide structure with any desired accuracy, the proposed model can be used in particular for design optimization. Furthermore, the Lagrangian formulation provides for: (i) a clear identification of the mathematical source of amplification, (ii) exact expressions for the conserved energy and its flux distributions obtained from the Noether theorem. In the case of uniform MTLs we carry out an exhaustive analysis of eigenmodes and find sharp conditions on the parameters of the system to provide for amplifying regimes

Quantitative thermodynamic model for globular protein folding

We present a statistical mechanics formalism for theoretical description of the process of protein folding ↔ unfolding transition in water environment. The formalism is based on the construction of the partition function of a protein obeying two-stage-like folding kinetics. Using the statistical mechanics model of solvation of hydrophobic hydrocarbons we obtain the partition function of infinitely diluted solution of proteins in water environment. The calculated dependencies of the protein heat capacities upon temperature are compared with the corresponding results of experimental measurements for staphylococcal nuclease and metmyoglobin