34 research outputs found
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 â 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