Molecular Dynamics Simulations of Bio-Nano Systems with MBN Explorer

AbstractWe present results of molecular dynamics simulations performed using a multi-purpose computer code MBN Explorer. In particular we consider the process of laser induced acoustic desorption of lysine amino acids from the surface of a nickel foil. We analyze the rate of lysine desorption from the nickel foil at different foil accelerations and suggest a simple theoretical model to describe the observed results. We note that despite the universality, the computational efficiency of MBN Explorer is comparable (and in some cases even higher) than the computational efficiency of other software packages, making MBN Explorer a possible alternative to the available codes

Formalism of collective electron excitations in fullerenes

We present a detailed formalism for the description of collective electron excitations in fullerenes in the process of the electron inelastic scattering. Considering the system as a spherical shell of a finite width, we show that the differential cross section is defined by three plasmon excitations, namely two coupled modes of the surface plasmon and the volume plasmon. The interplay of the three plasmons appears due to the electron diffraction of the fullerene shell. Plasmon modes of different angular momenta provide dominating contributions to the differential cross section depending on the transferred momentum.Comment: 11 pages, 2 figures; submitted to the special issue "Atomic Cluster Collisions: Structure and Dynamics from the Nuclear to the Biological Scale" of Eur. Phys. J.

Radial doses around energetic ion tracks and the onset of shock waves on the nanoscale

Abstract: Energetic ions lose their energy in tissue mainly by ionising its molecules. This produces secondary electrons which transport this energy radially away from the ion path. The ranges of most of these electrons do not exceed a few nanometres, therefore large energy densities (radial doses) are produced within a narrow region around the ion trajectory. Large energy density gradients correspond to large pressure gradients and this brings about shock waves propagating away from the ion path. Previous works have studied these waves by molecular dynamics (MD) simulations investigating their damaging effects on DNA molecules. However, these simulations where performed assuming that all energy lost by ions is deposited uniformly in thin cylinders around their path. In the present work, the radial dose distributions, calculated by solving the diffusion equation for the low energy electrons and complemented with a semi-empirical inclusion of more energetic δ-electrons, are used to set up initial conditions for the shock wave simulation. The effect of these energy distributions vs. stepwise energy distributions in tracks on the strength of shock waves induced by carbon ions both in the Bragg peak region and out of it is studied by MD simulations

The influence of the structure imperfectness of a crystalline undulator on the emission spectrum

We study the influence of an imperfect structure of a crystalline undulator on the spectrum of the undulator radiation. The main attention is paid to the undulators in which the periodic bending in the bulk appears as a result of a regular (periodic) surface deformations. We demonstrate that this method of preparation of a crystalline undulator inevitably leads to a variation of the bending amplitude over the crystal thickness and to the presence of the subharmonics with smaller bending period. Both of these features noticeably influence the monochromatic pattern of the undulator radiation.Comment: 26 pages, 9 figures, IOP style, submitted to NIM

Simulation of the ion-induced shock waves effects on the transport of chemically reactive species in ion tracks

Abstract: The passage of energetic ions through tissue initiates a series of physico-chemical events which leads to biodamage. The study of such ion-induced biodamage using a multiscale approach to the physics of radiation damage with ions has led to the prediction of shock waves being initiated by concentrated energy deposition along the ion track. In this work the radial energy deposition around carbon ion paths, calculated solving diffusion equations, is augmented with the inclusion of more energetic δ-electrons. The radial profiles of energy deposition and the induced concentrations of free radicals are used to simulate the shock waves by means of reactive classical molecular dynamics, which predict a characteristic distribution of reactive chemical species which may have an as yet unrecognised contribution to the nascent biodamage. The paper also suggests some experimental methods by which such a shock wave may be detected and the predictions of these simulations verified

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

Double strand breaks in DNA resulting from double-electron-emission events

A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two electrons, making such a mechanism possible. This effect qualitatively solves a puzzle of large yields of DSBs following irradiation of DNA molecules. The transport of secondary electrons, including the additional electrons, is studied in relation to the assessment of radiation damage due to incident ions. This work is a stage in the inclusion of Auger mechanism and like effects into the multiscale approach to ion-beam cancer therapy.Comment: 4 pages, 3 figure

Gold nanoparticles for cancer radiotherapy: a review

Radiotherapy is currently used in around 50% of cancer treatments and relies on the deposition of energy directly into tumour tissue. Although it is generally effective, some of the deposited energy can adversely affect healthy tissue outside the tumour volume, especially in the case of photon radiation (gamma and X-rays). Improved radiotherapy outcomes can be achieved by employing ion beams due to the characteristic energy deposition curve which culminates in a localised, high radiation dose (in form of a Bragg peak). In addition to ion radiotherapy, novel sensitisers, such as nanoparticles, have shown to locally increase the damaging effect of both photon and ion radiation, when both are applied to the tumour area. Amongst the available nanoparticle systems, gold nanoparticles have become particularly popular due to several advantages: biocompatibility, well-established methods for synthesis in a wide range of sizes, and the possibility of coating of their surface with a large number of different molecules to provide partial control of, for example, surface charge or interaction with serum proteins. This gives a full range of options for design parameter combinations, in which the optimal choice is not always clear, partially due to a lack of understanding of many processes that take place upon irradiation of such complicated systems. In this review, we summarise the mechanisms of action of radiation therapy with photons and ions in the presence and absence of nanoparticles, as well as the influence of some of the core and coating design parameters of nanoparticles on their radiosensitisation capabilities

Random walk approximation for the radial dose dependence

We investigate the properties of the radial distribution of energy deposited by ions, calculated using a random walk approach, which is an important analytical tool for solving transport problems. This investigation is motivated by the desire to understand the range of applicability of the random walk approximation for problems related to radiation damage assessment. We study the radial dose at small and moderate distances and compare our results to the results of Monte Carlo simulations