Energetic Cluster Research Articles

Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase.

The Orthoflavivirus NS3 helicase (NS3h) is crucial in virus replication, representing a potential drug target for pathogenesis. NS3h utilizes nucleotide triphosphate (ATP) for hydrolysis energy to translocate on single-stranded nucleic acids, which is an important step in the unwinding of double-stranded nucleic acids. Intermediate states along the ATP hydrolysis cycle and conformational changes between these states, represent important yet difficult-to-identify targets for potential inhibitors. Extensive molecular dynamics simulations of West Nile virus NS3h+ssRNA in the apo, ATP, ADP+Piand ADP bound states were used to model the conformational ensembles along this cycle. Energetic and structural clustering analyses depict a clear trend of differential enthalpic affinity of NS3h with ADP, demonstrating a probable mechanism of hydrolysis turnover regulated by the motif-VI loop (MVIL). Based on these results, MVIL mutants (D471L, D471Nand D471E) were found to have a substantial reduction in ATPase activity and RNA replication compared to the wild-type. Simulations of the mutants in the apo state indicate a shift in MVIL populations favoring either a closed or open 'valve' conformation, affecting ATP entry or stabilization, respectively. Combining our molecular modeling with experimental evidence highlights a conformation-dependent role for MVIL as a 'valve' for the ATP-pocket, presenting a promising target for antiviral development.

Surface engineering by rogue wave induced by energetic carbon clusters

Swift heavy ions are effective in nanostructuring material surfaces. The irradiation of lanthanum fluoride with 30 MeV C60 leads to the creation of surface nanohillocks of size larger than the ones produced by monoatomic heavy ions. The generation of the observed nano-sized hillocks is described here by a new approach that is based on ion-induced intensive electronic excitations that create localized rogue waves. Consequently, the induced nonlinear ion-acoustic rogue waves are considered a hallmark of nanohillock formation. Plasma hydrodynamic equations produce a relationship between normalised electron number density and crystal lattice spacing. Similarities to the hillock profile suggest the crucial primary role of electron density in the fabrication of surface nanostructures.

An N-body/hydrodynamical simulation study of the merging cluster El Gordo: A compelling case for self-interacting dark matter?

We used a large set N-body/hydrodynamical simulations to study the physical properties of the merging cluster El Gordo. We find that the observed X-ray structures, along with other data, can be matched fairly well by simulations with collision velocities 2000 km s−1 ≲ V ≲ 2500 km s−1 and impact parameters 600 kpc ≲ P ≲ 800 kpc. The mass of the primary is constrained to be between ∼1015 M⊙ and ∼1.6 × 1015 M⊙, in accordance with recent lensing-based mass measurements. Moreover, a returning, post-apocenter, scenario is not supported by our head-on simulations. We also considered merger models that incorporate dark matter self-interactions. The simulation results show that the observed spatial offsets between the different mass components are well reproduced in self-interacting dark matter models with an elastic cross-section in the range σDM/mX ∼ 4 − 5 cm2 gr−1. In addition, the mean relative line-of-sight radial velocity between the two brightest cluster galaxies is found to be on the order of several hundred km s−1. We argue that these findings provide an unambiguous signature of a dark matter behavior that exhibits collisional properties in a very energetic high-redshift cluster collision. The range of allowed values we find for σDM/mX is, however, inconsistent with present upper limits. To resolve this tension, we suggest the possibility that the self-interacting dark matter model used here be considered as only a low-order approximation, and that the underlying physical processes that describe the interaction of dark matter in major cluster mergers are more complex than can be adequately represented by the commonly assumed approach based on the scattering of dark matter particles.

Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision.

The bombardment of a protein multilayer target by an energetic argon cluster ion beam enables protein transfer onto a collector in the vacuum while preserving their bioactivity (iBEAM method). In parallel to this new soft-landing variant, protein transfer in the gas phase is a prerequisite for their characterization by mass spectrometry. The successful transfer of bioactive lysozymes (14 kDa) by cluster-induced soft landing and its mechanistic explanation by molecular dynamics (MD) simulations have sparked an important inquiry: Can heavier biomolecules be desorbed while maintaining their tridimensional structure and hence their bioactivity? To address this question, we employed MD simulations using a reactive force field (ReaxFF). Specifically, the Ar cluster-induced desorption of glucose oxidase from either a gold substrate or a lysozyme underlayer was modeled using the LAMMPS code. First, the force field parameters were trained by computing the dissociation energetics of a series of organic molecules with ReaxFF and DFT, in order to realistically describe N-S and O-S interactions in the bombarded glucose oxidase molecule. Second, bombardment simulations investigated the effects of cluster size (ranging from 1000 to 10000 Ar atoms) and kinetic energy (1.5 and 3.0 eV/atom) on the structural features and energetics of the desorbing glucose oxidase. Our results show that large argon clusters (≥7000) are needed to desorb glucose oxidase from a gold surface, yet protein fragmentation and/or pronounced denaturation occur. However, the transfer of structurally preserved glucose oxidase in the gas phase is predicted by the simulations when an organic layer is used as a substrate.

Impact of electrical current on cluster nucleation production: Phase, structure, and nanosize for Al2O3

The aluminum industry clearly stands out for its versatility and relevance to the development of an entire production chain that generates thousands of jobs. This metal is present in everyone's daily life because it is used in a variety of industries, including civil construction, the automotive industry, health care, and energy. Nano alumina products were prepared in two different phases with different sizes, and shapes via a solid–liquid plasma reactor. Both yields were prepared in identical circumstances, but with different effects of electrical current that result in different energetic cluster formations that lead to different formation shapes, sizes and phase structures (γ-Al2O3-NPs and δ-Al2O3-Nano-structure). In our best knowledge, the most recent research carried out to obtain Al2O3-Nps by arc discharge successfully produced different shapes or phases in each experiment: γ-δ-θ-α-Al2O3-Nps that’s why studying the parameters that affect the shape formation of Nano-Al2O3 is among our research interests. The binary yields produced were characterized to investigate their shape, size, purity, and morphology. Furthermore, γ-Al2O3-NPs had a spherical shape with a diameter of about 41.5 nm, as opposed to the rhomboid shape of 30 nm for δ-Al2O3-NanoStructure. Results showed that the electrical current plays a vital role in the size and crystal structure of the nanoparticles. Based on current production, the composition and formation mechanisms of nanoparticles are discussed. This research demonstrates an eco-friendly route for the rapid production of various Nano-alumina structures. The discrepancy between the energy used and the work function to remove electrons may be converted to heat energy in solution or may be a key factor in altering the crystal order of the generated ions to achieve a certain shape.

Interactions of Cellular Energetic Gene Clusters in the Alzheimer's Mouse Brain.

Alzheimer's disease (AD) is the most common cause of dementia in the aging population. The pathological characteristics include extracellular senile plaques and intracellular neurofibrillary tangles. In addition, mitochondrial dysfunction, oxidative stress, and neuroinflammation contribute to AD pathogenesis. In this study, we sought to determine the crosstalk between different pathways in the brain of 5XFAD mice, a mouse model for amyloid pathology, by RNA-seq analysis. We observed significant changes in the expression of genes (1288 genes; adj p value < 0.05; log2-fold > 1 and < 1) related to pathways including oxidation-reduction, oxidative phosphorylation, innate immune response, ribosomal protein synthesis, and ubiquitin proteosome system. The most striking feature was the downregulation of genes related to oxidation-reduction process with changes in the expression of a large number of mitochondrial genes. We also observed an upregulation of several immune response genes. Gene interaction network of oxidation-reduction related genes further confirmed a tight cluster of mitochondrial genes. Furthermore, gene interaction analysis of all the 1288 genes showed at least three distinct interaction clusters, with the predominant one relating to cellular energetics. In summary, we identified 1288 genes distinctly different in the 5XFAD brain compared to the WT brain and found cellular energetics to be the most distinct gene cluster in the AD mouse brain.

Growth of nanocrystalline graphite on sapphire by implantation of large carbon clusters from SNICS source

Nano-crystalline graphite (NCG) structures on insulating layers have been grown via implantation of kilo-electron-volt (keV) energetic carbon clusters (Cn) on sapphire (Al2O3) and post-implantation thermal annealing conditions. The clusters were produced using a source of negative ion using Cesium sputtering (SNICS) with graphite and carbon nanotubes (CNT) as cathode materials. The Graphite cathode exhibited high currents for most of the cluster sizes. However, the CNT cathodes showed higher yields for relative heavy clusters (n = 16, 18, and 20). Also, carbon clusters as large as n ~ 56 were observed from the SNICS source. The Sapphire substrates were implanted with carbon cluster (Cn, n = 18) ions at 11 keV (~611 eV per carbon atom) with fluences of 1.1 × 1015 C18-clusters/cm2 (~2 × 1016 carbon atoms/cm2). Ion impact craters and surface build-ups were observed. Further, we have studied the carbon bonding characteristics by Raman Spectroscopy (RS) on as-implanted and annealed implanted samples. We have observed well-developed disorder (D), graphite (G), and 2D peaks from the optimized samples, indicating the formation of nano-crystalline graphite (NCG) structures on the surface. The ratio of D and G peaks in the RS spectra suggests that the nano-crystalline cluster diameter or in-plane correlation length is about 10–16.5 nm. The Crystal size approaches a maximum value with increasing post-implantation thermal annealing temperature. We have studied the growth of NCG by X-ray Photoelectron Spectroscopy (XPS) for the chemical bonding and distribution. The average sizes of crystalline NCGs were also estimated using Grazing Angle X-ray Diffraction (GAXRD) Spectrometry. The surface morphology of the implanted samples was investigated using Atomic Force Microscopy (AFM).

Computer Simulation of the Cluster Structure of an Oxygen-Octahedral Lithium Niobate Crystal

We have performed a computer simulation of processes taking place at formation of energetic equilibrium oxygen-octahedral clusters in a ferroelectric phase of a lithium niobate crystal (LN, LiNbO3). In order to do so we used a semiclassical atomistic model with a qualitative approach. For the first time we have modeled lithium niobate structure on the basis of oxygen octahedra, while unit cells are usually used. We have established that there is an energy efficient cluster size with a specific structure that approaches a congruent LN structure. We have also proved that stoichiometric composition of LN leads to loss of electrical neutrality; thus achievement of demanded properties including photorefractive ones is possible by doping. We have chosen an ion with a charge 3+ to build a model.

Secondary ion mass spectrometry using energetic cluster ion beams: Toward highly sensitive imaging mass spectrometry

Imaging mass spectrometry (IMS), based on linking mass-analysis data for ions and their original positions in a sample, allows the visualization of the spatial distribution of atomic and/or molecular species in the sample, and is therefore an essential analytical method for the characterization of chemical and biological materials. For sensitive elemental and chemical imaging using IMS, a sufficient amount of ions to be analyzed should be supplied from the analyzing area on the sample surface. Secondary ion mass spectrometry (SIMS) using energetic cluster ions (ECIs) with energies of sub-MeV and above as primary ions (ECI-SIMS) can provide the secondary ions necessary for the characterization of organic materials with high emission yields. Hence, ECI-SIMS is a good method for highly sensitive IMS. We report recent progress in ECI beam manipulation techniques for applications of ECI-SIMS to highly sensitive IMS together with the characteristics of ECI impacts on organic materials.

Freestanding and Supported MoS2 Monolayers under Cluster Irradiation: Insights from Molecular Dynamics Simulations.

Two-dimensional (2D) materials with nanometer-size holes are promising systems for DNA sequencing, water purification, and molecule selection/separation. However, controllable creation of holes with uniform sizes and shapes is still a challenge, especially when the 2D material consists of several atomic layers as, e.g., MoS2, the archetypical transition metal dichalcogenide. We use analytical potential molecular dynamics simulations to study the response of 2D MoS2 to cluster irradiation. We model both freestanding and supported sheets and assess the amount of damage created in MoS2 by the impacts of noble gas clusters in a wide range of cluster energies and incident angles. We show that cluster irradiation can be used to produce uniform holes in 2D MoS2 with the diameter being dependent on cluster size and energy. Energetic clusters can also be used to displace sulfur atoms preferentially from either top or bottom layers of S atoms in MoS2 and also clean the surface of MoS2 sheets from adsorbents. Our results for MoS2, which should be relevant to other 2D transition metal dichalcogenides, suggest new routes toward cluster beam engineering of devices based on 2D inorganic materials.

Molecular Dynamics Simulations of Vacancy Generation and Migration near a Monocrystalline Silicon Surface during Energetic Cluster Ion Implantation

The process of ion implantation often involves vacancy generation and migration. The vacancy generation and migration near a monocrystalline silicon surface during three kinds of energetic Si35 cluster ion implantations were investigated by molecular dynamics simulations in the present work. The patterns of vacancy generation and migration, as well as the implantation-induced amorphous structure, were analyzed according to radial distribution function, Wigner–Seitz cell, and identify diamond structure analytical methods. A lot of vacancies rapidly generate and migrate in primary directions and form an amorphous structure in the first two picoseconds. The cluster with higher incident kinetic energy can induce the generation and migration of more vacancies and a deeper amorphous structure. Moreover, boundaries have a loading–unloading effect, where interstitial atoms load into the boundary, which then acts as a source, emitting interstitial atoms to the target and inducing the generation of vacancies again. These results provide more insight into doping silicon via ion implantation.

Improved Modleach By Using More Energetic Cluster Head Selection Technique

Improved Modleach By Using More Energetic Cluster Head Selection Technique

Cluster beams, nano-ripples, and bio applications

Gas cluster ions are aggregates of weakly bonded gas atoms or molecules. Upon the impact of an energetic gas cluster ion, multiple collisions occur between the target atoms and the atoms in the cluster ion. These impact processes are completely different from those of a collision-cascade process induced by a single atomic or molecular (monomer) ion. Although the impact process of gas cluster ions is different, ripples similar to those formed by monomer ions are formed by gas cluster ion impacts at oblique incidence. In this review, ripple formation by gas cluster ions is discussed with respect to their formation mechanism, characteristics, and applications as biosensors.

Relationship between Energetic Performance and Clustering Effects on Incremental Nitramine Groups: A Theoretical Perspective.

Nitramine compounds are typical high-energy-density materials (HEDMs) and are widely used as explosives because of their superior explosive performance over conventional energetic materials. In this work, the thermal properties of 1-nitropiperidine (NPIP), 1,4-dinitropiperazine (DNP), and 1,3,5-trinitro-1,3,5-triazinane (RDX) were investigated from quantum mechanics (QM) and reactive force field (ReaxFF) molecular dynamics simulations. We found that the bond dissociation energy of the N-NO2 bond, heat of formation, released energy, produced fragments, and oxygen balance are closely related to the incremental nitramine group. The nitramine group has a significant effect on the energetic performance of these nitramine compounds. In addition, the increase of the nitramine group will improve thermal decomposition activity, promote the generation of small molecules, and restrain the formation of carbon clusters. We hope that this work can shed new light on the design of energetic materials.

A model for sputtering from solid surfaces bombarded by energetic clusters

Abstract A model is developed to explain and predict the sputtering from solid surfaces bombarded by energetic clusters, on the basis of shock wave generated at the impact of cluster. Under the shock compression the temperature increases causing the vaporization of material that requires an internal energy behind the shock, at least, of about twice the cohesive energy of target. The sputtering is treated as a gas of vaporized particles from a hemispherical volume behind the shock front. The sputter yield per cluster atoms is given as a universal function depending on the ratio of target to cluster atomic density and the ratio of cluster velocity to the velocity calculated on the basis of an internal energy equals about twice cohesive energy. The predictions of the model for self sputter yield of copper, gold, tungsten and of silver bombarded by C 60 clusters agree well, with the corresponding data simulated by molecular dynamics.

Irradiation effect on magnetic properties of FeRh thin films with energetic C60 cluster ion beam

Effect of energetic C60 cluster ion irradiation on magnetic properties in FeRh thin films was examined by SQUID and XMCD measurements. The XMCD signal for the C60 irradiated samples is larger than that for the C1 samples in the initial stage of the irradiation. In contrast, as for the irradiation with larger ion fluence, the XMCD spectrum for the sample irradiated with C1 ion is larger than that for the sample irradiated with C60 cluster ion. Although the magnetization for the C60 irradiation samples continuously decreases with increasing in the ion fluence, the saturation magnetization for the C1 irradiation samples increases with increasing in the ion fluence. Considering these different behaviors in the irradiation induced ferromagnetism, the cluster ion can effectively deposit the apparent elastic collision energy at the surface region in the film, which effectively causes the ferromagnetic state at the surface of the films.

Transfer-free synthesis of graphene-like atomically thin carbon films on SiC by ion beam mixing technique

Abstract Here we demonstrate the synthesis of graphene directly on SiC substrates at 900 °C using ion beam mixing technique with energetic carbon cluster ions on Ni/SiC structures. The thickness of 7–8 nm Ni films was evaporated on the SiC substrates, followed by C cluster ion bombarding. Carbon cluster ions C4 were bombarded at 16 keV with the dosage of 4 × 1016 atoms/cm2. After thermal annealing process Ni silicides were formed, whereas C atoms either from the decomposition of the SiC substrates or the implanted contributes to the graphene synthesis by segregating and precipitating process. The limited solubility of carbon atoms in silicides, involving SiC, Ni2Si, Ni5Si2, Ni3Si, resulted in diffusion and precipitation of carbon atoms to form graphene on top of Ni and the interface of Ni/SiC. The ion beam mixing technique provides an attractive production method of a transfer-free graphene growth on SiC and be compatible with current device fabrication.

Self-Organization of Amorphous Carbon Nanocapsules into Diamond Nanocrystals Driven by Self-Nanoscopic Excessive Pressure under Moderate Electron Irradiation without External Heating.

Phase transformation between carbon allotropes usually requires high pressures and high temperatures. Thus, the development of low-temperature phase transition approaches between carbon allotropes is highly desired. Herein, novel amorphous carbon nanocapsules are successfully synthesized by pulsed plasma glow discharge. These nanocapsules are comprised of highly strained carbon clusters encapsulated in a fullerene-like carbon matrix, with the formers serving as nucleation sites. These nucleation sites favored the formation of a diamond unit cell driven by the self-nanoscopic local excessive pressure, thereby significantly decreasing the temperature required for its transformation into a diamond nanocrystal. Under moderate electron beam irradiation (10-20 A cm-2 ) without external heating, self-organization of the energetic carbon clusters into diamond nanocrystals is achieved, whereas the surrounding fullerene-like carbon matrix remains nearly unchanged. Molecular dynamics simulations demonstrate that the defective rings as the active sites dominate the phase transition of amorphous carbon to diamond nanocrystal. The findings may open a promising route to realize phase transformation between carbon allotropes at a lower temperature.

Molecular dynamics simulations with electronic stopping can reproduce experimental sputtering yields of metals impacted by large cluster ions

An unsolved problem in research of sputtering from metals induced by energetic large cluster ions is that molecular dynamics (MD) simulations often produce sputtering yields much higher than experimental results. Different from the previous simulations considering only elastic atomic interactions (nuclear stopping), here we incorporate inelastic electrons–atoms interactions (electronic stopping, ES) into MD simulations using a friction model. In this way we have simulated continuous 45° impacts of 10–20keV C60 on a Ag(111) surface, and found that the calculated sputtering yields can be very close to the experimental results when the model parameter is appropriately assigned. Conversely, when we ignore the effect of ES, the yields are much higher, just like the previous studies. We further expand our research to the sputtering of Au induced by continuous keV C60 or Ar100 bombardments, and obtain quite similar results. Our study indicates that the gap between the experimental and the simulated sputtering yields is probably induced by the ignorance of ES in the simulations, and that a careful treatment of this issue is important for simulations of cluster-ion-induced sputtering, especially for those aiming to compare with experiments.

Enhanced microwave-absorption performance of FeCoB/Polyimide-Graphene composite by electric field modulation

Graphene was incorporated into polyimide resin to obtain Polyimide-Graphene polymer sheet via in-situ polymerization method. FeCoB nanoparticles, generated by a high energetic cluster deposition system, were then deposited on the Polyimide-Graphene sheets by electric field assisted deposition technology to form FeCoB/Polyimide-Graphene ternary composites. An electric field of about 5–30 kV was applied on the sample platform when the composites were manufactured. The strong magnetic properties of the composites were revealed by the measurement of hysteresis loops at room temperature. Then the laminated FeCoB/Polyimide(-Graphene) composites were used to perform reflection loss scan. It is found that the addition of a small amount of graphene promote the improvement of electromagnetic properties by increasing dielectric loss. And the cover of FeCoB films can dramatically enhance the microwave absorption capacity by enriching interfacial polarization effect and electromagnetic match. The results prove that the electric field assisted deposition technique is a very attractive avenue to enhance the microwave absorption performance of the ternary composite expressed by tuning their dielectric and magnetic properties.