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.

Ion beam processing of DNA origami nanostructures.

DNA origami nanostructures are emerging as a bottom-up nanopatterning approach. Direct combination of this approach with top-down nanotechnology, such as ion beams, has not been considered because of the soft nature of the DNA material. Here we demonstrate that the shape of 2D DNA origami nanostructures deposited on Si substrates is well preserved upon irradiation by ion beams, modeling ion implantation, lithography, and sputtering conditions. Structural changes in 2D DNA origami nanostructures deposited on Si are analyzed using AFM imaging. The observed effects on DNA origami include structure height decrease or increase upon fast heavy ion irradiation in vacuum and in air, respectively. Slow- and medium-energy heavy ion irradiation results in the cutting of the nanostructures or crater formation with ion-induced damage in the 10 nm range around the primary ion track. In all these cases, the designed shape of the 2D origami nanostructure remains unperturbed. Present stability and nature of damages on DNA origami nanostructures enable fusion of DNA origami advantages such as shape and positioning control into novel ion beam nanofabrication approaches.

Different Mechanisms of DNA Radiosensitization by 8-Bromoadenosine and 2'-Deoxy-2'-fluorocytidine Observed on DNA Origami Nanoframe Supports.

DNA origami nanoframes with two parallel DNA sequences are used to evaluate the effect of nucleoside substituents on radiation-induced DNA damage. Double strand breaks (DSB) of DNA are counted using atomic force microscopy (AFM), and total number of lesions is evaluated using real-time polymerase chain reaction (RT-PCR). Enhanced AT or GC content does not increase the number of DNA strand breaks. Incorporation of 8-bromoadenosine results in the highest enhancement in total number of lesions; however, the highest enhancement in DSB is observed for 2'-deoxy-2'-fluorocytidine, indicating different mechanisms of radiosensitization by nucleoside analogues with the halogen substituent on base or sugar moieties, respectively. "Bystander" effects are observed, when the number of DSB in a sequence is enhanced by a substituent in the parallel DNA sequence. The present approach eliminates limitations of previously developed methods and motivates detailed studies of poorly understood conformation or bystander effects in radiation induced damage to DNA.

Electron attachment to microhydrated 4-nitro- and 4-bromo-thiophenol.

We investigate the effect of microhydration on electron attachment to thiophenols with halogen (Br) and nitro (NO2) functional groups in the para position. We focus on the formation of anions upon the attachment of low-energy electrons with energies below 8 eV to heterogeneous clusters of the thiophenols with water. For nitro-thiophenol (NTP), the primary reaction channel observed is the associative electron attachment, irrespective of the microhydration. On the other hand, bromothiophenol (BTP) fragments significantly upon the electron attachment, producing Br- and (BTP-H)- anions. Microhydration suppresses fragmentation of both molecules, however in bromothiophenol, the Br- channel remains intense and Br(H2O)n- hydrated fragment clusters are observed. The results are supported by the reaction energetics obtained from ab initio calculations. Different dissociation dynamics of NTP and BTP can be related to different products of their plasmon induced reactions on Au nanoparticles. Computational modeling of the simplified BTP(H2O) system indicates that the electron attachment products reflect the structure of neutral precursor clusters - the anion dissociation dynamics is controlled by the hydration site.

Folding DNA into origami nanostructures enhances resistance to ionizing radiation.

We report experimental results on damage induced by ionizing radiation to DNA origami triangles which are commonly used prototypes for scaffolded DNA origami nanostructures. We demonstrate extreme stability of DNA origami upon irradiation, which is caused by (i) the multi-row design holding the shape of the origami even after severe damage to the scaffold DNA and (ii) the reduction of damage to the scaffold DNA due to the protective effect of the folded structure. With respect to damage induced by ionizing radiation, the protective effect of the structure is superior to that of a naturally paired DNA double helix. Present results allow estimating the stability of scaffolded DNA origami nanostructures in applications such as nanotechnology, pharmacy or in singulo molecular studies where they are exposed to ionizing radiation from natural and artificial sources. Additionally, possibilities are opened for scaffolded DNA use in the design of radiation-resistant and radio-sensitive materials.

Response under low-energy electron irradiation of a thin film of a potential copper precursor for focused electron beam induced deposition (FEBID).

Background: Focused electron beam induced deposition (FEBID) allows for the deposition of free standing material within nanometre sizes. The improvement of the technique needs a combination of new precursors and optimized irradiation strategies to achieve a controlled fragmentation of the precursor for leaving deposited material of desired composition. Here a new class of copper precursors is studied following an approach that probes some surface processes involved in the fragmentation of precursors. We use complexes of copper(II) with amines and perfluorinated carboxylate ligands that are solid and stable under ambient conditions. They are directly deposited on the surface for studying the fragmentation with surface science tools. Results: Infrared spectroscopy and high-resolution electron energy loss spectroscopy (HREELS) are combined to show that the precursor is able to spontaneously lose amine ligands under vacuum. This loss can be enhanced by mild heating. The combination of mass spectrometry and low-energy electron irradiation (0-15 eV) shows that full amine ligands can be released upon irradiation, and that fragmentation of the perfluorinated ligands is induced by electrons of energy as low as 1.5 eV. Finally, the cross section for this process is estimated from the temporal evolution in the experiments on electron-stimulated desorption (ESD). Conclusion: The release of full ligands under high vacuum and by electron irradiation, and the cross section measured here for ligands fragmentation allow one to envisage the use of the two precursors for FEBID studies.

Electron Processing at 50 eV of Terphenylthiol Self-Assembled Monolayers: Contributions of Primary and Secondary Electrons.

Aromatic self-assembled monolayers (SAMs) can serve as platforms for development of supramolecular assemblies driven by surface templates. For many applications, electron processing is used to locally reinforce the layer. To achieve better control of the irradiation step, chemical transformations induced by electron impact at 50 eV of terphenylthiol SAMs are studied, with these SAMs serving as model aromatic SAMs. High-resolution electron energy loss spectroscopy (HREELS) and electron-stimulated desorption (ESD) of neutral fragment measurements are combined to investigate electron-induced chemical transformation of the layer. The decrease of the CH stretching HREELS signature is mainly attributed to dehydrogenation, without a noticeable hybridization change of the hydrogenated carbon centers. Its evolution as a function of the irradiation dose gives an estimate of the effective hydrogen content loss cross-section, σ = 2.7-4.7 × 10(-17) cm(2). Electron impact ionization is the major primary mechanism involved, with the impact electronic excitation contributing only marginally. Therefore, special attention is given to the contribution of the low-energy secondary electrons to the induced chemistry. The effective cross-section related to dissociative secondary electron attachment at 6 eV is estimated to be 1 order of magnitude smaller. The 1 eV electrons do not induce significant chemical modification for a 2.5 mC cm(-2) dose, excluding their contribution.