Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment.

This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions.

Role of the Molecular Environment in Quenching the Irradiation-Driven Fragmentation of Fe(CO): A Reactive Molecular Dynamics Study.

Irradiation-driven fragmentation and chemical transformations of molecular systems play a key role in nanofabrication processes where organometallic compounds break up due to the irradiation with focused particle beams. In this study, reactive molecular dynamics simulations have been performed to analyze the role of the molecular environment on the irradiation-induced fragmentation of molecular systems. As a case study, we consider the dissociative ionization of iron pentacarbonyl, Fe(CO), a widely used precursor molecule for focused electron beam-induced deposition.

Multiscale modeling of stochastic dynamics processes with MBN Explorer.

Stochastic dynamics describes processes in complex systems having the probabilistic nature. They can involve very different dynamical systems and occur on very different temporal and spatial scale. This paper discusses the concept of stochastic dynamics and its implementation in the popular program MBN Explorer.

Atomistic simulation of the FEBID-driven growth of iron-based nanostructures.

The growth of iron-containing nanostructures in the process of focused electron beam-induced deposition (FEBID) of Fe(CO) is studied by means of atomistic irradiation-driven molecular dynamics (IDMD) simulations. The geometrical characteristics (lateral size, height and volume), morphology and metal content of the grown nanostructures are analyzed at different irradiation and precursor replenishment conditions corresponding to the electron-limited and precursor-limited regimes (ELR & PLR) of FEBID. A significant variation of the deposit's morphology and elemental composition is observed with increasing the electron current from 1 to 4 nA.

Molecular dynamics simulation of nanofilament breakage in neuromorphic nanoparticle networks.

Neuromorphic computing systems may be the future of computing and cluster-based networks are a promising architecture for the realization of these systems. The creation and dissolution of synapses between the clusters are of great importance for their function. In this work, we model the thermal breakage of a gold nanofilament located between two gold nanoparticles via molecular dynamics simulations to study on the mechanisms of neuromorphic nanoparticle-based devices.

Molecular Dynamics Characterization of Radiosensitizing Coated Gold Nanoparticles in Aqueous Environment.

Functionalized metal nanoparticles (NPs) have been proposed as promising radiosensitizing agents for more efficient radiotherapy treatment using photons and ion beams. Radiosensitizing properties of NPs may depend on many different parameters (such as size, composition, and density) of the metal core, the organic coatings, and the molecular environment. A systematic exploration of each of these parameters on the atomistic level remains a formidable and costly experimental task, but it can be addressed by means of advanced computational modeling.

Lethal DNA damage caused by ion-induced shock waves in cells.

The elucidation of fundamental mechanisms underlying ion-induced radiation damage of biological systems is crucial for advancing radiotherapy with ion beams and for radiation protection in space. The study of ion-induced biodamage using the phenomenon-based multiscale approach (MSA) to the physics of radiation damage with ions has led to the prediction of nanoscale shock waves created by ions in a biological medium at the high linear energy transfer (LET). The high-LET regime corresponds to the keV and higher-energy losses by ions per nanometer, which is typical for ions heavier than carbon at the Bragg peak region in biological media.

Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF).

This paper presents a detailed computational protocol for the atomistic simulation of formation and growth of metal-containing nanostructures during focused electron beam-induced deposition (FEBID). The protocol is based upon irradiation-driven molecular dynamics (IDMD), a novel and general methodology for computer simulations of irradiation-driven transformations of complex molecular systems by means of the advanced software packages MBN Explorer and MBN Studio. Atomistic simulations performed following the formulated protocol provide valuable insights into the fundamental mechanisms of electron-induced precursor fragmentation and the related mechanism of nanostructure formation and growth using FEBID, which are essential for the further advancement of FEBID-based nanofabrication.

Topical Issue on many particle spectroscopy of atoms, molecules, clusters and surfaces editorial: Editorial.

Many particle spectroscopy is a subject of continued interest to many experimental and theoretical groups worldwide. It is based on the coincidence spectroscopy of minimum two particles coming from the same elementary process. It is a very powerful tool for studying not just atoms and molecules but also more extended electronic systems such as clusters and surfaces.

Multiscale simulation of the focused electron beam induced deposition process.

Focused electron beam induced deposition (FEBID) is a powerful technique for 3D-printing of complex nanodevices. However, for resolutions below 10 nm, it struggles to control size, morphology and composition of the structures, due to a lack of molecular-level understanding of the underlying irradiation-driven chemistry (IDC). Computational modeling is a tool to comprehend and further optimize FEBID-related technologies.

Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field.

Ion-induced DNA damage is an important effect underlying ion beam cancer therapy. This article introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically it is demonstrated how single- and double strand breaks in a DNA molecule could be described by the reactive CHARMM (rCHARMM) force field implemented in the program MBN Explorer.

Modeling MesoBioNano systems with MBN Studio made easy.

This paper introduces MesoBioNano (MBN) Studio - a graphical user interface for a popular multiscale simulation package MBN Explorer. MBN Studio has been developed to facilitate setting up and starting MBN Explorer calculations, monitoring their progress and examining the calculation results. It is tailored for any calculations that are supported by MBN Explorer, such as for example the single-point energy calculations, structure optimization, molecular dynamics, and kinetic Monte Carlo simulations.

First principles simulation of damage to solvated nucleotides due to shock waves.

We present a first-principles molecular dynamics study of the effect of shock waves (SWs) propagating in a model biological medium. We find that the SW can cause chemical modifications through varied and complex mechanisms, in particular, phosphate-sugar and sugar-base bond breaks. In addition, the SW promotes the dissociation of water molecules, thus enhancing the ionic strength of the medium.

A New Standard DNA Damage (SDD) Data Format.

Our understanding of radiation-induced cellular damage has greatly improved over the past few decades. Despite this progress, there are still many obstacles to fully understand how radiation interacts with biologically relevant cellular components, such as DNA, to cause observable end points such as cell killing. Damage in DNA is identified as a major route of cell killing.

[Sliding ingvinal haernias in children].

Aim: To study the features of diagnosis and treatment of children with sliding inguinal hernias.

Material And Methods: 30-year experience of treatment of 19 boys with sliding inguinal hernia and 1 boy with bilateral sliding femoral hernia was analyzed.

Results: 14 out of all children with inguinal and femoral hernia admitted with the diagnosis of incarcerated inguinal hernia.

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).

Multiscale approach predictions for biological outcomes in ion-beam cancer therapy.

Ion-beam therapy provides advances in cancer treatment, offering the possibility of excellent dose localization and thus maximising cell-killing within the tumour. The full potential of such therapy can only be realised if the fundamental mechanisms leading to lethal cell damage under ion irradiation are well understood. The key question is whether it is possible to quantitatively predict macroscopic biological effects caused by ion radiation on the basis of physical and chemical effects related to the ion-medium interactions on a nanometre scale.

Reconciling simulated melting and ground-state properties of metals with a modified embedded-atom method potential.

We propose a modification of the embedded-atom method-type potential aiming at reconciling simulated melting and ground-state properties of metals by means of classical molecular dynamics. Considering titanium, magnesium, gold, and platinum as case studies, we demonstrate that simulations performed with the modified force field yield quantitatively correctly both the melting temperature of the metals and their ground-state properties. It is shown that the accounting for the long-range interatomic interactions noticeably affects the melting point assessment.

Thermomechanical effects caused by heavy ions propagating in tissue.

The thermomechanical effects caused by ions propagating in tissue are discussed. Large energy densities in small regions surrounding ion paths cause shock waves propagating in tissue. The strength of the shock waves depends on the linear energy transfer.

Revealing the mechanism of the low-energy electron yield enhancement from sensitizing nanoparticles.

We provide a physical explanation for the enhancement of the low-energy electron production by sensitizing nanoparticles due to irradiation by fast ions. It is demonstrated that a significant increase in the number of emitted electrons arises from the collective electron excitations in the nanoparticle. We predict a new mechanism of the yield enhancement due to the plasmon excitations and quantitatively estimate its contribution to the electron production.

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample.

Validation of classical force fields for the description of thermo-mechanical properties of transition metal materials.

It is demonstrated that classical force fields validated through the density functional theory (DFT) calculations of small titanium and nickel clusters can be applied for the description of thermo-mechanical properties of corresponding materials. This has been achieved by means of full-atom molecular dynamics simulations of nanoindentation of amorphous and nanostructured Ti and Ni-Ti materials. The theoretical analysis performed and comparison with experimental data demonstrate that the utilized classical force fields for Ti-Ti, Ni-Ni and Ni-Ti interactions describe reasonably well hardness and the Young's modulus of these materials.

Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics.

Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest.

Multiscale physics of ion-induced radiation damage.

This is a review of a multiscale approach to the physics of ion-beam cancer therapy, an approach suggested in order to understand the interplay of a large number of phenomena involved in the radiation damage scenario occurring on a range of temporal, spatial, and energy scales. We describe different effects that take place on different scales and play major roles in the scenario of interaction of ions with tissue. The understanding of these effects allows an assessment of relative biological effectiveness that relates the physical quantities, such as dose, to the biological values, such as the probability of cell survival.