A. C. T. van Duin

Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine

The application of atmospheric pressure plasmas in medicine is increasingly gaining attention in recent years, although very little is currently known about the plasma-induced processes occurring on the surface of living organisms. It is known that most bio-organisms, including bacteria, are coated by a liquid film surrounding them, and there might be many interactions between plasma species and the liquid layer before the plasma species reach the surface of the bio-organisms. Therefore, it is essential to study the behaviour of the reactive species in a liquid film, in order to determine whether these species can travel through this layer and reach the biomolecules, or whether new species are formed along the way. In this work, we investigate the interaction of reactive oxygen species (i.e. O, OH, HO2 and H2O2) with water, which is assumed as a simple model system for the liquid layer surrounding biomolecules. Our computational investigations show that OH, HO2 and H2O2 can travel deep into the liquid layer and are hence in principle able to reach the bio-organism. Furthermore, O, OH and HO2 radicals react with water molecules through hydrogen-abstraction reactions, whereas no H-abstraction reaction takes place in the case of H2O2. This study is important to gain insight into the fundamental operating mechanisms in plasma medicine, in general, and the interaction mechanisms of plasma species with a liquid film, in particular.

Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls

In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. C-O, C-N and C-C bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale.

Graphene to fluorographene and fluorographane: a theoretical study

We report here a fully reactive molecular dynamics study on the structural and dynamical aspects of the fluorination of graphene membranes (fluorographene). Our results show that fluorination tends to produce defective areas on the graphene membranes with significant distortions of carbon-carbon bonds. Depending on the amount of incorporated fluorine atoms, large membrane holes were observed due to carbon atom losses. These results may explain the broad distribution of the structural lattice parameter values experimentally observed. We have also investigated the effects of mixing hydrogen and fluorine atoms on the graphene functionalization. Our results show that, when in small amounts, the presence of hydrogen atoms produces a significant decrease in the rate of fluorine incorporation onto the membrane. On the other hand, when fluorine is the minority element, it produces a significant catalytic effect on the rate of hydrogen incorporation. We have also observed the spontaneous formation of new hybrid structures with different stable configurations (chair-like, zigzag-like and boat-like) which we named fluorographane.

First-principles studies on vacancy-modified interstitial diffusion mechanism of oxygen in nickel, associated with large-scale atomic simulation techniques

This paper is concerned with the prediction of oxygen diffusivities in fcc nickel from first-principles calculations and large-scale atomic simulations. Considering only the interstitial octahedral to tetrahedral to octahedral minimum energy pathway for oxygen diffusion in fcc lattice, greatly underestimates the migration barrier and overestimates the diffusivities by several orders of magnitude. The results indicate that vacancies in the Ni-lattice significantly impact the migration barrier of oxygen in nickel. Incorporation of the effect of vacancies results in predicted diffusivities consistent with available experimental data. First-principles calculations show that at high temperatures the vacancy concentration is comparable to the oxygen solubility, and there is a strong binding energy and a redistribution of charge density between the oxygen atom and vacancy. Consequently, there is a strong attraction between the oxygen and vacancy in the Ni lattice, which impacts diffusion.

Atomic-scale insight into the interactions between hydroxyl radicals and DNA in solution using the ReaxFF reactive force field

Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma–cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered time-scale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution.

Can amorphization take place in nanoscale interconnects

The trend of miniaturization has highlighted the problems of heat dissipation and electromigration in nanoelectronic device interconnects, but not amorphization. While amorphization is known to be a high pressure and/or temperature phenomenon, we argue that defect density is the key factor, while temperature and pressure are only the means. For nanoscale interconnects carrying modest current density, large vacancy concentrations may be generated without the necessity of high temperature or pressure due to the large fraction of grain boundaries and triple points. To investigate this hypothesis, we performed in situ transmission electron microscope (TEM) experiments on 200 nm thick (80 nm average grain size) aluminum specimens. Electron diffraction patterns indicate partial amorphization at modest current density of about 10(5) A cm(-2), which is too low to trigger electromigration. Since amorphization results in drastic decrease in mechanical ductility as well as electrical and thermal conductivity, further increase in current density to about 7 × 10(5) A cm(-2) resulted in brittle fracture failure. Our molecular dynamics (MD) simulations predict the formation of amorphous regions in response to large mechanical stresses (due to nanoscale grain size) and excess vacancies at the cathode side of the thin films. The findings of this study suggest that amorphization can precede electromigration and thereby play a vital role in the reliability of micro/nanoelectronic devices.

Study of ice cluster impacts on amorphous silica using the ReaxFF reactive force field molecular dynamics simulation method

We study the dynamics of the collisions between amorphous silica structures and amorphous and crystal ice clusters with impact velocities of 1 km/s, 4 km/s, and 7 km/s using the ReaxFF reactive molecular dynamics simulation method. The initial ice clusters consist of 150 water molecules for the amorphous ice cluster and 128 water molecules for the crystal ice cluster. The ice clusters are collided on the surface of amorphous fully oxidized and suboxide silica. These simulations show that at 1 km/s impact velocities, all the ice clusters accumulate on the surface and at 4 km/s and 7 km/s impact velocities, some of the ice cluster molecules bounce back from the surface. At 4 km/s and 7 km/s impact velocities, few of the water molecules dissociations are observed. The effect of the second ice cluster impacts on the surfaces which are fully covered with ice, on the mass loss/accumulation is studied. These studies show that at 1 km/s impacts, the entire ice cluster accumulates on the surface at both first and ...

Deuterium uptake and sputtering of simultaneous lithiated, boronized, and oxidized carbon surfaces irradiated by low-energy deuterium

We study the effects of deuterium irradiation on D-uptake by simultaneously boronized, lithiated, oxidized, and deuterated carbon surfaces. We present analysis of the bonding chemistry of D for various concentrations of boron, lithium, oxygen, and deuterium on carbon surfaces using molecular dynamics with reactive force field potentials, which are here adapted to include the interaction of boron and lithium. We calculate D retention and sputtering yields of each constituent of the Li-C-B-O mixture and discuss the role of oxygen in these processes. The extent of the qualitative agreement between new experimental data for B-C-O-D obtained in this paper and computational data is provided. As in the case of the Li-C-O system, comparative studies where experimental and computational data complement each other (in this case on the B-Li-C-O system) provide deeper insights into the mechanisms behind the role that O plays in the retention of D, a relevant issue in fusion machines.

Molecular dynamics simulation of Al grain mixing in Fe/Ni matrices and its influence on oxidation

AlxNiyFe(1−x−y) alloys are structural materials with potential application in high-temperature oxidizing environments. These materials are of specific interest as they have the ability to develop an oxidation resistant surface layer. To study diffusion and oxidation processes related to this surface layer formation, the mixing behavior of different sized Al grains in pure Ni and Fe matrices, with approximate grain/matrix atom ratio of 1:3, at temperatures above and below the structure melting point, was studied using ReaxFF-based molecular dynamics simulations. The simulations have been carried out at constant pressure, with temperatures being stepwise ramped over the range of 300-3000 K. For the Ni matrix, our results indicated lower chemical strain energy for Al in the mixed alloy and completion of mixing at a lower temperature for the Fe matrix. These results confirm that the Al-Ni alloy is energetically more stable than the Al-Fe alloy, which is in agreement with experiment. Further, larger Al grains ...

Molecular Dynamics Studies to Understand the Mechanism of Heat Accommodation in Homogeneous Condensing Flow of CO2

In the present work, we investigate the accuracy of the heat accommodation model, used in a meso‐scale discrete particle BGK based condensation model for studying the homogeneous condensing flow of CO2. It was found in those studies that the heat accommodation model played a key role in the numerical reproduction of the experiments. The major assumption made in such a heat accommodation model was the instantaneous release of heat of condensation to the gas particles in a cell. In the present work, we examine the veracity of the assumption used in the heat accommodation model, and understand the heat accommodation mechanism in general. To this end, we have used the atomistic molecular dynamics method to study the gas‐cluster interactions from a fundamental standpoint. It is found that the time taken by gas‐cluster interactions to establish an equilibrium from an initial state of non‐equilibrium is less than the time step used in meso‐scale analysis [1]. We also find that a dynamic equilibrium is establishe...