Abstract: The adsorption, dissociation, and diffusion of CO2 on the anatase (001) surface was studied using DFT by means of the generalized gradient approximation using the Perdew−Burcke−Ernzerhof (PBE)-functional and applying corrections for long-range dispersion interactions. Different stable adsorption configurations were identified for the fully oxidized surface. The most stable adsorption configuration is the monodentated carbonate-like structure. Small energy barriers were identified for the conversion of a physisorbed to a chemisorbed configuration.
CO2 dissociation is found to be unfeasible on the stoichiometric surface. The introduction of oxygen vacancy defects gives rise to new highly stable adsorption configurations with a stronger activation of the C−O bonds. This leads to the possibility of exothermic dissociation of CO2 with barriers up to 22.2 kcal/mol,
corresponding to chemical lifetimes of less than 4 s at 300 K. These reactions cause a CO molecule to be formed, which will easily desorb, and the reduced surface to become oxidized. It is clear that oxygen vacancy defects play a key role in the catalytic activity of an anatase (001) surface. Oxygen vacancies play an important role in the dissociation of CO2 on the anatase (001) surface, and will play a significant role in complex problems, such as the catalytic conversion of CO2 to value-added chemicals.

Abstract: A method has been developed for damage-free cesium (Cs) encapsulation within single-walled carbon nanotubes (SWNTs) with fine position selectivity. Precise energy tuning of Cs-ion irradiation revealed that there is a clear energy window (2060 eV) for the efficient encapsulation of Cs through the hexagonal network of SWNT sidewalls without causing significant damage. This minimum energy threshold of Cs-ion encapsulation (∼20 eV) matches well with the value obtained by ab initio simulation (∼22 eV). Furthermore, position-selective Cs encapsulation was carried out, resulting in the successful formation of pn-junction SWNT thin films with excellent environmental stability.

Abstract: Immobilization of single metal atoms on a solid host opens numerous possibilities for catalyst designs. If that host is a two-dimensional sheet, sheet curvature becomes a design parameter potentially complementary to host and metal composition. Here, we use a combination of density functional theory calculations and microkinetic modeling to compare the mechanisms and kinetics of formic acid decomposition and formation, chosen for their relevance as a potential hydrogen storage medium, over single Ru atoms anchored to pyridinic nitrogen in a planar graphene flake (RuN4-G) and curved carbon nanotube (RuN4-CNT). Activation barriers are lowered and the predicted turnover frequencies are increased over RuN4-CNT relative to RuN4-CNT. The results highlight the potential of curvature control as a means to achieve high performance and robust catalysts.

Abstract: In this work, we use density functional theory calculations to study the combined effect of external electric fields, surface morphology, and surface charge on CO2 activation over Cu(111), Cu(211), Cu(110), and Cu(001) surfaces. We observe that the binding energy of the CO2 molecule on Cu surfaces increases significantly upon increasing the applied electric field strength. In addition, rougher surfaces respond more effectively to the presence of the external electric field toward facilitating the formation of a carbonate-like CO2 structure and the transformation of the most stable adsorption mode from physisorption to chemisorption. The presence of surface charges further strengthens the electric field effect and consequently causes an improved bending of the CO2 molecule and C−O bond length elongation. On the other hand, a net charge in the absence of an externally applied electric field shows only a marginal effect on CO2 binding. The chemisorbed CO2 is more stable and further activated when the effects of an external electric field, rough surface, and surface charge are combined. These results can help to elucidate the underlying factors that control CO2 activation in heterogeneous and plasma catalysis, as well as in electrochemical processes.

Abstract: The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of reactive processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics.

Abstract: The continuous miniaturization of nanodevices, such as transistors, solar cells, and optical fibers, requires the controlled synthesis of (ultra)thin gate oxides (<10 nm), including Si gate-oxide (SiO2) with high quality at the atomic scale. Traditional thermal growth of SiO2 on planar Si surfaces, however, does not allow one to obtain such ultrathin oxide due to either the high oxygen diffusivity at high temperature or the very low sticking ability of incident oxygen at low temperature. Two recent techniques, both operative at low (room) temperature, have been put forward to overcome these obstacles: (i) hyperthermal oxidation of planar Si surfaces and (ii) thermal or plasma-assisted oxidation of nonplanar Si surfaces, including Si nanowires (SiNWs). These nanooxidation processes are, however, often difficult to study experimentally, due to the key intermediate processes taking place on the nanosecond time scale.
In this Account, these Si nano-oxidation techniques are discussed from a computational point of view and compared to both hyperthermal and thermal oxidation experiments, as well as to well-known models of thermal oxidation, including the Deal−Grove, Cabrera−Mott, and Kao models and several alternative mechanisms. In our studies, we use reactive molecular dynamics (MD) and hybrid MD/Monte Carlo simulation techniques, applying the Reax force field. The incident energy of oxygen species is chosen in the range of 1−5 eV in hyperthermal oxidation of planar Si surfaces in order to prevent energy-induced damage. It turns out that hyperthermal growth allows for two growth modes, where the ultrathin oxide thickness depends on either (1) only the kinetic energy of the incident oxygen species at a growth temperature below Ttrans = 600 K, or (2) both the incident energy and the growth temperature at a growth temperature above Ttrans. These modes are specific to such ultrathin oxides, and are not observed in traditional thermal oxidation, nor theoretically considered by already existing models. In the case of thermal or plasma-assisted oxidation of small Si nanowires, on the other hand, the thickness of the ultrathin oxide is a function of the growth temperature and the nanowire diameter. Below Ttrans, which varies with the nanowire diameter, partially oxidized SiNW are formed, whereas complete oxidation to a SiO2 nanowire occurs only above Ttrans. In both nano-oxidation processes at lower temperature (T < Ttrans), final sandwich c-Si|SiOx|a-SiO2 structures are obtained due to a competition between overcoming the energy barrier to penetrate into Si subsurface layers and the compressive stress (∼2−3 GPa) at the Si crystal/oxide interface. The overall atomic-simulation results strongly indicate that the thickness of the intermediate SiOx (x < 2) region is very limited (∼0.5 nm) and constant irrespective of oxidation parameters. Thus, control over the ultrathin SiO2 thickness with good quality is indeed possible by accurately tuning the oxidant energy, oxidation temperature and surface curvature.
In general, we discuss and put in perspective these two oxidation mechanisms for obtaining controllable ultrathin gate-oxide films, offering a new route toward the fabrication of nanodevices via selective nano-oxidation.

Abstract: The limitation in time and length scale is a major issue of molecular dynamics (MD) simulation. Although several methods have been developed to extend the MD time scale, their performance usually deteriorates with increasing system size. Therefore, an acceleration method which is applicable to large systems is required to bridge the gap between the MD simulations and target phenomena. In this study, an accelerated MD method for large system is developed based on the collective variable-driven hyperdynamics (CVHD) method [K.M. Bal and E.C. Neyts, 2015]. The key idea is to run CVHD in parallel with rate control and accelerate multiple possible events simultaneously. Using this novel method, carbon diffusion in bcc-iron bicrystal with grain boundary is examined as an application for practical materials. Carbon atoms reaching at the grain boundary are trapped whereas carbon atoms in the bulk region diffuse randomly, and both dynamic regimes can be simultaneously accelerated with the parallel CVHD technique.

Abstract: Plasma catalysis continues to gain increasing scientific interest, both in established fields like toxic waste abatement and emerging fields like greenhouse gas conversion into value-added chemicals. Attention is typically focused on the obtained conversion process selectivity, rates and energy efficiency. Much less attention is usually paid to the underlying mechanistic aspects of the processes that occur. In this contribution, we critically examine a number of fundamentally important nanoscale thermodynamic aspects of plasma catalysis, which are very relevant to these processes but so far have been overlooked or insufficiently covered in the plasma catalysis literature.

Abstract: The free energy surface (FES) for carbon segregation from nickel nanoparticles is obtained from advanced molecular dynamics simulations. A suitable reaction coordinate is developed that can distinguish dissolved carbon atoms from segregated dimers, chains and junctions on the nanoparticle surface. Because of the typically long segregation time scale (up to ms), metadynamics simulations along the developed reaction coordinate are used to construct FES over a wide range of temperatures and carbon concentrations. The FES revealed the relative stability of different stages in the segregation process, and free energy barriers and rates of the individual steps could then be calculated and decomposed into enthalpic and entropic contributions. As the carbon concentration in the nickel nanoparticle increases, segregated carbon becomes more stable in terms of both enthalpy and entropy. The activation free energy of the reaction also decreases with the increase of carbon concentration, which can be mainly attributed to entropic effects. These insights and the methodology developed to obtain them improve our understanding of carbon segregation process across materials science in general, and the nucleation and growth of carbon nanotube in particular.

Abstract: In order to optimize the plasma-synthesis and modification process of carbon nanomaterials for applications such as nanoelectronics and energy storage, a deeper understanding of fundamental hydrogengraphite/graphene interactions is required. Atomistic simulations by Molecular Dynamics have proven to be indispensable to illuminate these phenomena. However, severe time-scale limitations restrict them to very fast processes such as reflection, while slow thermal processes such as surface diffusion and molecular desorption are commonly inaccessible. In this work, we could however reach these thermal processes for the first time at time-scales and surface temperatures (1000 K) similar to high-flux plasma exposure experiments during the simulation of multilayer graphene etching by 5 eV H ions. This was achieved by applying the Collective Variable-Driven Hyperdynamics biasing technique, which extended the inter-impact time over a range of six orders of magnitude, down to a more realistic ion-flux of 1023m
2s
1. The results show that this not only causes a strong shift from predominant ion-to thermally induced interactions, but also significantly affects the hydrogen uptake and surface evolution. This study thus elucidates H ion-graphite/graphene interaction mechanisms and stresses the importance of including long time-scales in atomistic simulations at high surface temperatures to understand the dynamics of the ion-surface system.

Abstract: Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability.
Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane.
Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage.
General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play.

Abstract: tWe investigate microdischarge formation inside catalyst pores by a two-dimensional fluid model forvarious pore sizes in the m-range and for various applied voltages. Indeed, this is a poorly understoodphenomenon in plasma catalysis. The calculations are performed for a dielectric barrier discharge inhelium, at atmospheric pressure. The electron and ion densities, electron temperature, electric field andpotential, as well as the electron impact ionization and excitation rate and the densities of excited plasmaspecies, are examined for a better understanding of the characteristics of the plasma inside a pore. Theresults indicate that the pore size and the applied voltage are critical parameters for the formation of amicrodischarge inside a pore. At an applied voltage of 20 kV, our calculations reveal that the ionizationmainly takes place inside the pore, and the electron density shows a significant increase near and inthe pore for pore sizes larger than 200m, whereas the effect of the pore on the total ion density isevident even for 10m pores. When the pore size is fixed at 30m, the presence of the pore has nosignificant influence on the plasma properties at an applied voltage of 2 kV. Upon increasing the voltage,the ionization process is enhanced due to the strong electric field and high electron temperature, andthe ion density shows a remarkable increase near and in the pore for voltages above 10 kV. These resultsindicate that the plasma species can be formed inside pores of structured catalysts (in the m range),and they may interact with the catalyst surface, and affect the plasma catalytic process.

Abstract: In this paper the various elementary plasma—surface interaction processes occurring in plasma catalysis are critically evaluated. Specifically, plasma catalysis at atmospheric pressure is considered. The importance of the various processes is analyzed for the most common plasma catalysis sources, viz. the dielectric barrier discharge and the gliding arc. The role and importance of surface chemical reactions (including adsorption, surface-mediated association and dissociation reactions, and desorption), plasma-induced surface modification, photocatalyst activation, heating, charging, surface discharge formation and electric field enhancement are discussed in the context of plasma catalysis. Numerous examples are provided to demonstrate the importance of the various processes.

Abstract: The presence of iodide ions during the growth of gold nanorods strongly affects the shape of the final products, which is proposed to be due to selective iodide adsorption on certain crystallographic facets. Therefore, a detailed structural and morphological characterization of the starting rods is crucial toward understanding this effect. Electron tomography is used to determine the crystallographic indices of the lateral facets of gold nanorods, as well as those present at the tips. Based on this information, density functional theory calculations are used to determine the surface and interface energies of the observed facets and provide insight into the relationship between the amount of iodide ions in the growth solution and the final morphology of anisotropic gold nanoparticles.