Modeling MesoBioNano systems with MBN Studio made easy

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.

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.

Local elastic properties of polystyrene nanocomposites increase significantly due to nonaffine deformations

We investigate the local elastic properties of polystyrene doped with SiO_{2} nanoparticles by analyzing the local density fluctuations. The density fluctuations were established from coarse-grained molecular dynamics simulations performed with the MARTINI force field. A significant increase in polystyrene stiffness was revealed within a characteristic range of 1.4 nm from the nanoparticle, while polystyrene density saturates to the bulk value at significantly shorter distances. The enhancement of the local elastic properties of the polymer was attributed to the effect of nonaffine deformations at the length scale below 1 nm, which was further confirmed through the random matrix model with variable strength of disorder.

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.

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.