62 research outputs found
Transport of secondary electrons and reactive species in ion tracks
The transport of reactive species brought about by ions traversing
tissue-like medium is analysed analytically. Secondary electrons ejected by
ions are capable of ionizing other molecules; the transport of these
generations of electrons is studied using the random walk approximation until
these electrons remain ballistic. Then, the distribution of solvated electrons
produced as a result of interaction of low-energy electrons with water
molecules is obtained. The radial distribution of energy loss by ions and
secondary electrons to the medium yields the initial radial dose distribution,
which can be used as initial conditions for the predicted shock waves. The
formation, diffusion, and chemical evolution of hydroxyl radicals in liquid
water are studied as well.Comment: 7 pages 4 figure
Conformational changes in glycine tri- and hexapeptide
We have investigated the potential energy surfaces for glycine 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 the 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 the glycine 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: 23 pages, 9 figure
Molecular dynamics study of the stability of a carbon nanotube atop a catalytic nanoparticle
The stability of a single-walled carbon nanotube placed on top of a catalytic
nickel nanoparticle is investigated by means of molecular dynamics simulations.
As a case study, we consider the nanotube consisting of 720 carbon
atoms and the icosahedral Ni cluster. An explicit set of
constant-temperature simulations is performed in order to cover a broad
temperature range from 400 to 1200 K, at which a successful growth of carbon
nanotubes has been achieved experimentally by means of chemical vapor
deposition. The stability of the system depending on parameters of the involved
interatomic interactions is analyzed. It is demonstrated that different
scenarios of the nanotube dynamics atop the nanoparticle are possible depending
on the parameters of the Ni-C potential. When the interaction is weak the
nanotube is stable and resembles its highly symmetric structure, while an
increase of the interaction energy leads to the abrupt collapse of the nanotube
in the initial stage of simulation. In order to validate the parameters of the
Ni-C interaction utilized in the simulations, DFT calculations of the potential
energy surface for carbon-nickel compounds are performed. The calculated
dissociation energy of the Ni-C bond is in good agreement with the values,
which correspond to the case of a stable and not deformed nanotube simulated
within the MD approach.Comment: 11 pages, 5 figures; submitted to Eur. Phys. J.
Channeling process in a bent crystal
We have investigated the channeling process of charged particles in a bent crystal. Invoking simple assumptions we derive a criterion, which determines whether channeling occurs or not. We obtain the same criterion using the Dirac equation. It is shown that the centrifugal force acting on the particle in the bent crystal significantly alters the effective transverse potential. The cases of axial and planar channeling are considered. The channeling probability and the dechanneling probability due to tunneling of the particle under the barrier in the effective transverse potential are estimated. These probabilities depend on the specific scaling parameter characterizing the process. Using the quasiclassical theory of synchrotron radiation we have calculated the contribution to the radiation spectrum, which arises due to the curvature of the channel. This contribution becomes significant to TeV electrons or positrons. Some practical consequences of our results are briefly discussed
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
Classical molecular dynamics simulations of fusion and fragmentation in fullerene-fullerene collisions
We present the results of classical molecular dynamics simulations of
collision-induced fusion and fragmentation of C fullerenes, performed by
means of the MBN Explorer software package. The simulations provide information
on structural differences of the fused compound depending on kinematics of the
collision process. The analysis of fragmentation dynamics at different initial
conditions shows that the size distributions of produced molecular fragments
are peaked for dimers, which is in agreement with a well-established mechanism
of C fragmentation via preferential C emission. Atomic trajectories
of the colliding particles are analyzed and different fragmentation patterns
are observed and discussed. On the basis of the performed simulations,
characteristic time of C emission is estimated as a function of collision
energy. The results are compared with experimental time-of-flight distributions
of molecular fragments and with earlier theoretical studies. Considering the
widely explored case study of C--C collisions, we demonstrate
broad capabilities of the MBN Explorer software, which can be utilized for
studying collisions of a broad variety of nanoscale and biomolecular systems by
means of classical molecular dynamics
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