arXiv subjects

Nigel J. Mason

Publications and source records attributed to Nigel J. Mason.

30 records · Page 2Linked to original sources

arXiv2022

Molecular dynamics characterisation of radiosensitising 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, organic coatings and the molecular environment. A systematic exploration of each of these parameters on the atomistic level remains a costly experimental task but it can be addressed by means of advanced computational modeling. This paper outlines a detailed computational procedure for the construction and atomistic-level characterization of radiosensitizing metal NPs in explicit molecular media. The procedure is general and extensible to many different combinations of the core, coating and environment. As an illustrative and experimentally relevant case study, we consider nanometre-sized gold NPs coated with thiol-poly(ethylene glycol)-amine molecules of different length and surface density and solvated in water at ambient conditions. 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 $\sim$3 molecules/nm$^{2}$ 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 to 3 nm from the gold surface depending on the length of ligands. 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.

physics.atm-clus↗

arXiv2021

The Ice Chamber for Astrophysics-Astrochemistry (ICA): A New Experimental Facility for Ion Impact Studies of Astrophysical Ice Analogues

The Ice Chamber for Astrophysics-Astrochemistry (ICA) is a new laboratory end-station located at the Institute for Nuclear Research (Atomki) in Debrecen, Hungary. The ICA has been specifically designed for the study of the physico-chemical properties of astrophysical ice analogues and their chemical evolution when subjected to ionising radiation and thermal processing. The ICA is an ultra-high vacuum compatible chamber containing a series of IR-transparent substrates mounted in a copper holder connected to a closed-cycle cryostat capable of being cooled down to 20 K, itself mounted on a 360° rotation stage and a z-linear manipulator. Ices are deposited onto the substrates via background deposition of dosed gases. Ice structure and chemical composition are monitored by means of FTIR absorbance spectroscopy in transmission mode, although use of reflectance mode is possible by using metallic substrates. Pre-prepared ices may be processed in a variety of ways. A 2 MV Tandetron accelerator is capable of delivering a wide variety of high-energy ions into the ICA, which simulates ice processing by cosmic rays, the solar wind, or magnetospheric ions. The ICA is also equipped with an electron gun which may be used for electron impact radiolysis of ices. Thermal processing of both deposited and processed ices may be monitored by means of both FTIR spectroscopy and quadrupole mass spectrometry. In this paper, we provide a detailed description of the ICA set-up, as well as an overview of preliminary results obtained and future plans.

astro-ph.IM↗

arXiv2021

Electron Irradiation and Thermal Chemistry Studies of Interstellar and Planetary Ice Analogues at the ICA Astrochemistry Facility

The modelling of molecular excitation and dissociation processes relevant to astrochemistry requires the validation of theories by comparison with data generated from laboratory experimentation. The newly commissioned Ice Chamber for Astrophysics-Astrochemistry (ICA) allows for the study of astrophysical ice analogues and their evolution when subjected to energetic processing, thus simulating the processes and alterations interstellar icy grain mantles and icy outer Solar System bodies undergo. ICA is an ultra-high vacuum compatible chamber containing a series of IR-transparent substrates upon which the ice analogues may be deposited at temperatures of down to 20 K. Processing of the ices may be performed in one of three ways: (i) ion impacts with projectiles delivered by a 2 MV Tandetron-type accelerator, (ii) electron irradiation from a gun fitted directly to the chamber, and (iii) thermal processing across a temperature range of 20-300 K. The physico-chemical evolution of the ices is studied in situ using FTIR absorbance spectroscopy and quadrupole mass spectrometry. In this paper, we present an overview of the ICA facility with a focus on characterising the electron beams used for electron impact studies, as well as reporting the preliminary results obtained during electron irradiation and thermal processing of selected ices.

astro-ph.IM↗

arXiv2021

The Role of Terahertz and Far-IR Spectroscopy in Understanding the Formation and Evolution of Interstellar Prebiotic Molecules

Stellar systems are often formed through the collapse of dense molecular clouds which, in turn, return copious amounts of atomic and molecular material to the interstellar medium. An in-depth understanding of chemical evolution during this cyclic interaction between the stars and the interstellar medium is at the heart of astrochemistry. Systematic chemical composition changes as interstellar clouds evolve from the diffuse stage to dense, quiescent molecular clouds to star-forming regions and proto-planetary disks further enrich the molecular diversity leading to the evolution of ever more complex molecules. In particular, the icy mantles formed on interstellar dust grains and their irradiation are thought to be the origin of many of the observed molecules, including those that are deemed to be prebiotic; that is those molecules necessary for the origin of life. This review will discuss both observational (e.g., ALMA, SOFIA, Herschel) and laboratory investigations using millimeter, submillimeter, and terahertz and far-IR (THz/F-IR) spectroscopies and the role that they play in contributing to our understanding of the formation of prebiotic molecules. Mid-IR spectroscopy has typically been the primary tool used in laboratory studies. However, THz/F-IR spectroscopy offers an additional and complementary approach in that it provides the ability to investigate intermolecular interactions compared to the intramolecular modes available in the mid-IR. THz/F-IR spectroscopy is still somewhat under-utilized, but with the additional capability it brings, its popularity is likely to significantly increase in the near future. This review will discuss the strengths and limitations of such methods, and will also provide some suggestions on future research areas that should be pursued in the coming decade exploiting both space-borne and laboratory facilities.

astro-ph.GA↗

arXiv2021

Systems Astrochemistry: A New Doctrine for Experimental Studies

Laboratory experiments play a key role in deciphering the chemistry of the interstellar medium (ISM) and the role that product complex organic molecules (COMs) may play in the origins of life. However, to date, most studies in experimental astrochemistry have made use of reductionist approaches to experimental design in which chemical responses to variations in a single parameter are investigated while all other parameters are held constant. Although such work does afford insight into the chemistry of the ISM, it is likely that several important points, such as the relative importance of an experimental parameter in determining the chemical outcome of a reaction and the interaction between parameters, remain ambiguous. In light of this, we propose adopting a new systems astrochemistry framework for experimental studies which draws on current work performed in the field of prebiotic chemistry, and present the basic tenants of such an approach in this article. This systems approach would focus on the emergent properties of the chemical system by performing the simultaneous variation of multiple experimental parameters and would allow for the effect of each parameter, as well as their interactions, to be quantified. We anticipate that the application of systems science to laboratory astrochemistry, coupled with developments in hyphenated analytical techniques and data analytics, will uncover significant new data hitherto unknown, and will aid in better linking laboratory experiments to observations and modelling work.

astro-ph.EP↗

arXiv2021

Sulfur Ice Astrochemistry: A Review of Laboratory Studies

Sulfur is the tenth most abundant element in the universe and is known to play a significant role in biological systems. Accordingly, in recent years there has been increased interest in the role of sulfur in astrochemical reactions and planetary geology and geochemistry. Among the many avenues of research currently being explored is the laboratory processing of astrophysical ice analogues. Such research involves the synthesis of an ice of specific morphology and chemical composition at temperatures and pressures relevant to a selected astrophysical setting (such as the interstellar medium or the surfaces of icy moons). Subsequent processing of the ice under conditions that simulate the selected astrophysical setting commonly involves radiolysis, photolysis, thermal processing, neutral-neutral fragment chemistry, or any combination of these, and has been the subject of several studies. The in-situ changes in ice morphology and chemistry occurring during such processing has been monitored via spectroscopic or spectrometric techniques. In this paper, we have reviewed the results of laboratory investigations concerned with sulfur chemistry in several astrophysical ice analogues. Specifically, we review (i) the spectroscopy of sulfur-containing astrochemical molecules in the condensed phase, (ii) atom and radical addition reactions, (iii) the thermal processing of sulfur-bearing ices, (iv) photochemical experiments, (v) the non-reactive charged particle radiolysis of sulfur-bearing ices, and (vi) sulfur ion bombardment of and implantation in ice analogues. Potential future studies in the field of solid phase sulfur astrochemistry are also discussed in the context of forthcoming space missions, such as the NASA James Webb Space Telescope and the ESA Jupiter Icy Moons Explorer mission.

astro-ph.EP↗

arXiv2018

Transport of secondary electrons through coatings of ion-irradiated metallic nanoparticles

The transport of low-energy electrons through the coating of a radiosensitizing metallic nanoparticle under fast ion irradiation is analyzed theoretically and numerically. As a case study, we consider a poly(ethylene glycol)-coated gold nanoparticle of diameter 1.6~nm excited by a carbon ion in the Bragg peak region in water as well as by more energetic carbon ions. The diffusion equation for low-energy electrons emitted from a finite-size spherical source representing the surface of the metal core is solved to obtain the electron number density as a function of radial distance and time. Information on the atomistic structure and composition of the coating is obtained from molecular dynamics simulations performed with the MBN Explorer software package. Two mechanisms of low-energy electron production by the metallic core are considered: the relaxation of plasmon excitations and collective excitations of valence $d$ electrons in individual atoms of gold. Diffusion coefficients and characteristic lifetimes of electrons propagating in gold, water, and poly(ethylene glycol) are obtained from relativistic partial wave analysis and the dielectric formalism, respectively. On this basis, the number of electrons released through the organic coating into the surrounding aqueous medium and the number of hydroxyl radicals produced are evaluated. The largest increase of the radical yield due to low-energy electrons is observed when the nanoparticle is excited by an ion with energy significantly exceeding that in the Bragg peak region. It is also shown that the water content of the coating, especially near the surface of the metal core, is crucial for the production of hydroxyl radicals.

physics.atm-clus↗

arXiv2017

QDB: a new database of plasma chemistries and reactions

One of the most challenging and recurring problems when modelling plasmas is the lack of data on key atomic and molecular reactions that drive plasma processes. Even when there are data for some reactions, complete and validated datasets of chemistries are rarely available. This hinders research on plasma processes and curbs development of industrial applications. The QDB project aims to address this problem by providing a platform for provision, exchange, and validation of chemistry datasets. A new data model developed for QDB is presented. QDB collates published data on both electron scattering and heavy-particle reactions. These data are formed into reaction sets, which are then validated against experimental data where possible. This process produces both complete chemistry sets and identifies key reactions that are currently unreported in the literature. Gaps in the datasets can be filled using established theoretical methods. Initial validated chemistry sets for SF$_6$/CF$_4$/O$_2$ and SF$_6$/CF$_4$/N$_2$/H$_2$ are presented as examples.

physics.plasm-ph↗

arXiv2017

The effect of ion-induced shock waves on the transport of reacting species around energetic ion tracks

The passage of energetic ions through tissue initiates a series of physico-chemical events, which lead to biodamage. The study of this scenario using a multiscale approach brought about the theoretical prediction of shock waves initiated by energy deposited within ion tracks. These waves are being explored in this letter in different aspects. The radial dose that sets their initial conditions is calculated using diffusion equations extended to include the effect of energetic $δ$-electrons. The resulting shock waves are simulated by means of reactive classical molecular dynamics. The simulations predict a characteristic distribution of reactive species which may have a significant contribution to biodamage, and also suggests experimental means to detect the shock waves.

physics.bio-ph↗

arXiv2017

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

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 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 molecular dynamics simulations.

physics.bio-ph↗

arXiv2016

Modeling of nanoparticle coatings for medical applications

Gold nanoparticles (AuNPs) have been shown to possess properties beneficial for the treatment of cancerous tumors by acting as radiosensitizers for both photon and ion radiation. Blood circulation time is usually increased by coating the AuNPs with poly(ethylene glycol) (PEG) ligands. The effectiveness of the PEG coating, however, depends on both the ligand surface density and length of the PEG molecules, making it important to understand the structure of the coating. In this paper the thickness, ligand surface density, and density of the PEG coating is studied with classical molecular dynamics using the software package MBN Explorer. AuNPs consisting of 135 atoms (approximately 1.4 nm diameter) in a water medium have been studied with the number of PEG ligands varying between 32 and 60. We find that the thickness of the coating is only weakly dependent on the surface ligand density and that the degree of water penetration increased when there is a smaller number of attached ligands.

physics.atm-clus↗

arXiv2016

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 lies beyond the possibilities of the analytical model.

physics.bio-ph↗