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. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.

Role of the Molecular Environment in Quenching the Irradiation-Driven Fragmentation of Fe(CO)5: 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)5, a widely used precursor molecule for focused electron beam-induced deposition. In connection to recent experiments, the irradiation-induced fragmentation dynamics of an isolated Fe(CO)5+ molecule is studied and compared with that of Fe(CO)5+ embedded into an argon cluster. The appearance energies of different fragments of isolated Fe(CO)5+ agree with the recent experimental data. For Fe(CO)5+ embedded into an argon cluster, the simulations reproduce the experimentally observed suppression of Fe(CO)5+ fragmentation and provide an atomistic-level understanding of this effect. Understanding irradiation-driven fragmentation patterns for molecular systems in environments facilitates the advancement of atomistic models of irradiation-induced chemistry processes involving complex molecular systems.

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. Stochastic dynamics in MBN Explorer relies on the Monte Carlo approach and permits simulations of physical, chemical, and biological processes. The paper presents the basic theoretical concepts underlying stochastic dynamics implementation and provides several examples highlighting its applicability to different systems, such as diffusing proteins seeking an anchor point on a cell membrane, deposition of nanoparticles on a surface leading to structures with fractal morphologies, and oscillations of compounds in an autocatalytic reaction. The chosen examples illustrate the diversity of applications that can be modeled by means of stochastic dynamics with 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)5 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. At low beam current (1 nA) corresponding to the ELR and a low degree of Fe(CO)5 fragmentation, the nanogranular structures are formed which consist of isolated iron clusters embedded into an organic matrix. In this regime, metal clusters do not coalesce with increasing electron fluence, resulting in relatively low metal content of the nanostructures. A higher beam current of 4 nA corresponding to the PLR facilitates the precursor fragmentation and the coalescence of metal clusters into a dendrite-like structure with the size corresponding to the primary electron beam. The IDMD simulations enable atomistic-level predictions on the nanoscopic characterization of the initial phase of nanostructure growth in the FEBID process. These predictions can be verified in high-resolution transmission electron microscopy experiments.

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. This paper describes a detailed computational procedure for construction and atomistic-level characterization of radiosensitizing metal NPs in explicit molecular media. The procedure is general and is extensible to many different combinations of the core, coating, and environment. As an illustrative and experimentally relevant case study, we consider nanometer-sized gold NPs coated with thiol-poly(ethylene glycol)-amine molecules of different length and surface density and solvated in water at ambient conditions. The radial distribution of different atoms in the coatings as well as distribution and structural properties of water around the coated NPs are analyzed and linked to radiosensitizing properties of the NPs. It is revealed that the structure of the coating layer on the solvated NPs depends strongly on the surface density of ligands. At surface densities below ∼3 molecules/nm2 the coating represents a mixture of different conformation states, whereas elongated "brush"-like structures are formed at higher densities of ligands. The water content in denser coatings is significantly lower at distances from 1 nm up to 3 nm from the gold surface depending on the length of ligand molecules. Such dense and thick coatings may suppress the production of hydroxyl radicals by low-energy electrons emitted from the metal NPs and thus diminish their radiosensitizing properties. The presented computational framework provides precise information for a quantitative atomistic-level description of the structural properties of coated metal NPs in biologically relevant environments and so may form a basis for future developments to achieve a more realistic description of irradiation-driven chemistry effects in the vicinity of coated metal NPs.

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. We employ simulations of Au nanowires of different lengths (20-80 Å), widths (4-8 Å) and shapes connecting two Au1415nanoparticles (NPs) and monitor the evolution of the system via a detailed structural identification analysis. We found that atoms of the nanofilament gradually aggregate towards the clusters, causing the middle of wire to gradually thin and then break. Most of the system remains crystalline during this process but the center is molten. The terminal NPs increase the melting point of the NWs by fixing the middle wire and act as recrystallization areas. We report a strong dependence on the width of the NWs, but also their length and structure. These results may serve as guidelines for the realization of cluster-based neuromorphic computing systems.

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. This paper reveals that the thermomechanical stress of the DNA molecule caused by the ion-induced shock wave becomes the dominant mechanism of complex DNA damage at the high-LET ion irradiation. Damage of the DNA molecule in water caused by a projectile-ion-induced shock wave is studied by means of reactive molecular dynamics simulations. Five projectile ions (carbon, oxygen, silicon, argon, and iron) at the Bragg peak energies are considered. For the chosen segment of the DNA molecule and the collision geometry, the number of DNA strand breaks is evaluated for each projectile ion as a function of the bond dissociation energy and the distance from the ion's path to the DNA strands. Simulations reveal that argon and especially iron ions induce the breakage of multiple bonds in a DNA double convolution containing 20 DNA base pairs. The DNA damage produced in segments of such size leads to complex irreparable lesions in a cell. This makes the shock-wave-induced thermomechanical stress the dominant mechanism of complex DNA damage at the high-LET ion irradiation. A detailed theory for evaluating the DNA damage caused by ions at high-LET is formulated and integrated into the MSA formalism. The theoretical analysis reveals that a single ion hitting a cell nucleus at high-LET is sufficient to produce highly complex, lethal damages to a cell by the shock-wave-induced thermomechanical stress. Accounting for the shock-wave-induced thermomechanical mechanism of DNA damage provides an explanation for the "overkill" effect observed experimentally in the dependence of cell survival probabilities on the radiation dose delivered with iron ions. This important observation provides strong experimental evidence of the ion-induced shock-wave effect and the related mechanism of radiation damage in cells.

Irradiation-driven molecular dynamics simulation of the FEBID process for Pt(PF3)4.

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. The developed computational methodology is general and applicable to different precursor molecules, substrate types, and irradiation regimes. The methodology can also be adjusted to simulate the nanostructure formation by other nanofabrication techniques using electron beams, such as direct electron beam lithography. In the present study, the methodology is applied to the IDMD simulation of the FEBID of Pt(PF3)4, a widely studied precursor molecule, on a SiO2 surface. The simulations reveal the processes driving the initial phase of nanostructure formation during FEBID, including the nucleation of Pt atoms and the formation of small metal clusters on the surface, followed by their aggregation and the formation of dendritic platinum nanostructures. The analysis of the simulation results provides spatially resolved relative metal content, height, and growth rate of the deposits, which represents valuable reference data for the experimental characterization of the nanostructures grown by FEBID.

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. Due to the large variety of its applications, it is really an interdisciplinary research field. This Topical Issue presents a state-of-the-art description of current research activities in the field of many particle spectroscopy. The contributions to this Issue represent original research results on both experimental and theoretical studies, involving the interaction of various projectiles, like photons, electrons, ions with atoms, molecules, 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. Here we utilize a novel multiscale methodology which couples Monte Carlo simulations for radiation transport with irradiation-driven molecular dynamics for simulating IDC with atomistic resolution. Through an in depth analysis of [Formula: see text] deposition on [Formula: see text] and its subsequent irradiation with electrons, we provide a comprehensive description of the FEBID process and its intrinsic operation. Our analysis reveals that simulations deliver unprecedented results in modeling the FEBID process, demonstrating an excellent agreement with available experimental data of the simulated nanomaterial composition, microstructure and growth rate as a function of the primary beam parameters. The generality of the methodology provides a powerful tool to study versatile problems where IDC and multiscale phenomena play an essential role.

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. The entire workflow of performing the shock wave simulations, including obtaining the crucial simulation parameters, is described in seven steps. Two exemplary analyses are provided for a case study simulation serving to: (a) quantify the shock wave propagation and (b) describe the dynamics of formation of DNA breaks. The article concludes by discussing the computational cost of the simulations and revealing the possible maximal computational time for different simulation set-ups.

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. Apart from that MBN Studio has built-in tools allowing the calculation and analysis of specific characteristics that are determined by the output of the simulations, such as the diffusion coefficients of molecular species, melting temperatures and associated heat capacities, radial distribution function; a dedicated modeling plug-in allows constructing molecular systems in a quick and efficient manner. Employing this plug-in, one can easily construct molecular systems of different geometries (e.g., spherical or ellipsoidal nanoparticles, cubic crystalline samples) with various atomic composition. The paper presents the first public release of MBN Studio and provides an overview of its significant capabilities, as well as the reference point for further extensions.

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. Freed protons can hydrolyze base and sugar rings previously opened by the shock. However, many of these events are only temporary, and bonds reform rapidly. Irreversible damage is observed for pressures above 15-20 GPa. These results are important to gain a better understanding of the microscopic damage mechanisms underlying cosmic-ray irradiation in space and ion-beam cancer therapy.

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.

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. We demonstrate that the phenomenon-based MultiScale Approach to the assessment of radiation damage with ions gives a positive answer to this question. We apply this approach to numerous experiments where survival curves were obtained for different cell lines and conditions. Contrary to other, in essence empirical methods for evaluation of macroscopic effects of ionising radiation, the MultiScale Approach predicts the biodamage based on the physical effects related to ionisation of the medium, transport of secondary particles, chemical interactions, thermo-mechanical pathways of biodamage, and heuristic biological criteria for cell survival. We anticipate this method to give great impetus to the practical improvement of ion-beam cancer therapy and the development of more efficient treatment protocols.

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. Molecular dynamics simulations help in determining the necessary strength of shock waves in order for the stresses caused by them to directly produce DNA strand breaks. At much smaller values of linear energy transfer, the shock waves may be instrumental in propagating reactive species formed close to the ion's path to large distances, successfully competing with diffusion.

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. Revealing the nanoscale mechanism of the electron yield enhancement, we provide an efficient tool for evaluating the yield of the emitted electron from various sensitizers. It is shown that the number of low-energy electrons generated by the gold and platinum nanoparticles of a given size exceeds that produced by the equivalent volume of water and by other metallic (e.g., gadolinium) nanoparticles by an order of magnitude. This observation emphasizes the sensitization effect of the noble-metal nanoparticles and endorses their application in novel technologies of cancer therapy with ionizing radiation.

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. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

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. The present article features an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system.

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. This observation is of the general nature and can be utilized for similar numerical exploration of thermo-mechanical properties of a broad range of materials.