Large Atomic Clusters Research Articles

Grain Growth Mechanism of CZTSSe Films Controlled by the Evaporation Area of Se

Thermally evaporated Se, including the molecules of Se2, Se5, Se6, Se7, and Se8 in the vapor at 550–600 °C, is widely used for the selenization of CZTSSe films. However, active small‐molecule Se2 tends to form large clusters of Se atoms at saturation vapor pressure, resulting in the large Se deficiency and poor crystallization of CZTSSe films. To regulate the time for Se to reach saturation vapor pressure and promote the role of active small‐molecule Se, the evaporation area of Se is controlled. Then the corresponding grain growth mechanism of CZTSSe films and device efficiency are systematically investigated. The results demonstrate that the appropriate evaporation area of Se can not only optimize the time for Se vapor to reach saturation, promote the rapid reaction crystallization between the precursor films and active Se2, but also inhibit the nucleation at the CZTSSe/Mo interface, thus making the CZTSSe films show a perfect top‐down grain growth mode. By preliminary optimization, when the evaporation area of Se is 245 mm2, a large‐grain spanning monolayer CZTSSe thin film is obtained; meanwhile, a device with a high efficiency of 12.39% is achieved. This study provides a new selenization strategy for improving the crystallinity of CZTSSe thin films.

Simulation of femtosecond laser ablation and spallation of titanium film based on two-temperature model and molecular dynamics

In order to study the interaction between a femtosecond laser and a titanium film, the method of combining the two-temperature model and molecular dynamics was used to simulate the ablation and spallation of the titanium film by the femtosecond laser with a wavelength of 800 nm. The spallation of the titanium film was explained from the perspective of the temperature and the stress wave. It is found that the femtosecond laser with a pulse width of 300 fs loads the titanium film, and the ablation threshold is around 0.05 J/cm2. The effects of different pulse widths in the range of 100–500 fs and different energy densities in the range of 0.10–0.20 J/cm2 on the spallation results of titanium films were also studied. We found that the femtosecond laser with a pulse width of 100 fs promotes the spallation phenomenon to occur more quickly. The surface spallation products of the titanium film were large clusters of atoms when the energy density is 0.10 J/cm2, but most of the surface spallation products of the titanium film were single atoms when the energy density is 0.20 J/cm2. These indicated that the energy density is an important factor affecting the spallation products of the titanium film. The evolution of maximum electron temperature, electron-lattice equilibrium temperature, and coupling time with pulse width and energy density are also given and analyzed. These results have important reference significance for studying the fracture and damage of titanium, and they help us to understand the mechanism of femtosecond laser processing materials.

Possible effects of fluxionality of a cavitand on its catalytic activity through confinement.

The discovery of fullerenes was a huge milestone in the scientific community, and with it came the urge to discover and analyze various small and large atomic and molecular clusters having a cavity. These cavitands of varied shapes and sizes have wide applications in the encapsulation of rare gas atoms to induce bond formation between them, storage of hydrogen and hydrocarbons to be used as alternative sources of fuel, catalyzation of otherwise slow reactions without using a catalyst, activation of small gas molecules, etc. Various cavitands like fullerenes, [ExBox]4+, cucurbit[n]urils, borospherenes, octa acid, etc. have been used for this purpose. Some clusters including cavitands exhibit fluxional behaviour. Systems in a confined environment often manifest interesting variations in their properties and behaviour, compared to their unconfined counterparts, facilitating the aforementioned applications. In this perspective article, we explore the possibility of making use of this extra degree of freedom, viz., the fluxionality, in changing the catalytic activity of the cavitand.

Cascades Damage in γ-Iron from Molecular Dynamics Simulations

The degradation of austenitic stainless steels under irradiation environment is a known problem for nuclear reactors, which starts from atoms displacement cascade. Here, molecular dynamics (MD) simulations have been used to investigate the formation of atomic displacement cascade in γ-iron for energies of the primary knock-on atom (PKA) up to 40 keV at 300 K. The number of Frenkel pairs increased sharply until a peak value was reached, which occurred at a time in the range of 0.1-2 ps. After that, a number of defects gradually decreased and became stabilized. Compared with α-iron, there was less defects in the stable stage, and more clustered defects were produced in γ-iron. Within the range of PKA energies, two regimes of power-law energy-dependence of the defect production were observed, which converge on 16.8 keV. The transition energy also marks the onset of the formation of large self-interstitial atom (SIA) clusters and vacancy clusters. Interstitial and vacancy clusters were in the form of Shockley, Frank dislocation loops and Stir-Rod dislocation loops.

Stochastic parallel algorithm of structural evolution of large Morse clusters

The formation of large Morse atomic clusters is a complex and time-consuming task, especially when the cluster stiffness equals 14. Currently, optimal cluster conformations are known for sizes up to 240 atoms. The article proposes a parallel stochastic algorithm for the structural evolution of Morse clusters, which makes it possible to find the optimal conformations of large atomic clusters. A significant number of problems associated with the complexity of the task are resolved using the proposed algorithm for optimizing the cluster structure. The results of optimization of Morse clusters for N> 240 are given.

Selenium Minerals: Structural and Chemical Diversity and Complexity

Chemical diversity of minerals containing selenium as an essential element has been analyzed in terms of the concept of mineral systems and the information-based structural and chemical complexity parameters. The study employs data for 123 Se mineral species approved by the International Mineralogical Association as of 25 May 2019. All known selenium minerals belong to seven mineral systems with the number of essential components ranging from one to seven. According to their chemical features, the minerals are subdivided into five groups: Native selenium, oxides, selenides, selenites, and selenates. Statistical analysis shows that there are strong and positive correlations between the chemical and structural complexities (measured as amounts of Shannon information per atom and per formula or unit cell) and the number of different chemical elements in a mineral. Analysis of relations between chemical and structural complexities provides strong evidence that there is an overall trend of increasing structural complexity with the increasing chemical complexity. The average structural complexity for Se minerals is equal to 2.4(1) bits per atom and 101(17) bits per unit cell. The chemical and structural complexities of O-free and O-bearing Se minerals are drastically different with the first group being simpler and the second group more complex. The O-free Se minerals (selenides and native Se) are primary minerals; their formation requires reducing conditions and is due to hydrothermal activity. The O-bearing Se minerals (oxides and oxysalts) form in near-surface environment, including oxidation zones of mineral deposits, evaporites and volcanic fumaroles. From the structural viewpoint, the five most complex Se minerals are marthozite, Cu(UO2)3(SeO3)2O2·8H2O (744.5 bits/cell); mandarinoite, Fe2(SeO3)3·6H2O (640.000 bits/cell); carlosruizite, K6Na4Na6Mg10(SeO4)12(IO3)12·12H2O (629.273 bits/cell); prewittite, KPb1.5ZnCu6O2(SeO3)2Cl10 (498.1 bits/cell); and nicksobolevite, Cu7(SeO3)2O2Cl6 (420.168 bits/cell). The mechanisms responsible for the high structural complexity of these minerals are high hydration states (marthozite and mandarinoite), high topological complexity (marthozite, mandarinoite, carlosruizite, nicksobolevite), high chemical complexity (prewittite and carlosruizite), and the presence of relatively large clusters of atoms (carlosruizite and nicksobolevite). In most cases, selenium itself does not play the crucial role in determining structural complexity (there are structural analogues or close species of marthozite, mandarinoite, and carlosruizite that do not contain Se), except for selenite chlorides, where stability of crystal structures is adjusted by the existence of attractive Se–Cl closed-shell interactions impossible for sulfates or phosphates. Most structurally complex Se minerals originate either from relatively low-temperature hydrothermal environments (as marthozite, mandarinoite, and carlosruizite) or from mild (500–700 °C) anhydrous gaseous environments of volcanic fumaroles (prewittite, nicksobolevite).

Mechanistic Insight into Gas Cluster-Induced Sputtering of Kilodalton Molecules Using Kinetic Energy Distribution Measurements

Recent progress in organic secondary ion mass spectrometry (SIMS) relied essentially on the development of new cluster beams, especially large atomic and molecular clusters formed via the adiabatic...

Practical approach for beryllium atomic clusters: TD-DFT potential energy surfaces from equilibrium to dissociation for excited states of 2s → 2p

To shed light on the spectroscopic energy-smearing mechanism of the recently developed technique for multi-element analysis (e.g., forensic tests on artworks), which is called plume laser-induced fluorescence, practically computer simulations need to be accurate and fast enough for generating wide-range excited-state potential energy surfaces (PESs) from equilibrium to dissociation of large (non-equilibrated) atomic clusters. Currently, all the very high-level post-Hartree–Fock theories (e.g., coupled-cluster theory) are computationally too expensive for this purpose (e.g., taking at least ~ 23 years). After considering the extensive applications of time-dependent density-functional theory (TD-DFT) in computing the optical properties of many-body systems, we wonder how TD-DFT performs in the wide-range-PES generations because no such TD-DFT application is found by us in the literature (perhaps due to its insufficient static/non-dynamical correlation energy). In this work, we carried out TD-DFT calculations on beryllium atomic clusters from Be1 to Be50 (in contrast to open-shell H2 or Li2 system, we think the individual closed-shell Be systems at the dissociation limit could help TD-DFT to describe the static/non-dynamical correlation. For example, it is usually considered that Be2 has zero non-dynamical correlation energy in the literature) with and without Tamm–Dancoff approximation (TDA). Electronic excited-state properties (e.g., PES, equilibrium position, dissociation energy, fork intersection) associated with 2s → 2p are systematically investigated at a total of 48 levels of TD-DFT. Our calculations are thoroughly benchmarked against experimental results and (very) high-level theoretical values. In short, we find that for accurate simulations, it is necessary to use diffuse basis sets and the TDA approximation. TD-DFT with the small basis set 3-21+G* took ~ 2 min to finish a single-point excitation energy calculation on a linear Be50 (a toy model), while the large basis set 6-311+G(2df,2p) took 30 min. By contrast, a couple-cluster theory EOM-CCSD with 6-311+G(2df,2p) took 2.5 h to do the same but merely for a smaller linear Be10. In general, we suggest that TD-DFT:TDA with 3-21+G* should be practically fast and accurate enough for emulating our desired wide-range excited-state PESs of large Be atomic clusters (including conical intersection points of close energies) in the future studies. Nevertheless, benchmarking work on (much) larger sizes of Be clusters will always be more desirable whenever its computational costs at very high level of theories becomes more tractable.

Superposition of Fragment Excitations for Excited States of Large Clusters with Application to Helium Clusters.

We develop a local excited-state method, based on the configuration interaction singles (CIS) wave function, for large atomic and molecular clusters. This method exploits the properties of absolutely localized molecular orbitals (ALMOs), which strictly limits the total number of excitations, and results in formal scaling with the third power of the system size for computing the full spectrum of ALMO-CIS excited states. The derivation of the equations and design of the algorithm are discussed in detail, with particular emphasis on the computational scaling. Clusters containing ∼500 atoms were used in evaluating the scaling, which agrees with the theoretical predictions, and the accuracy of the method is evaluated with respect to standard CIS. A pioneering application to the size dependence of the helium cluster spectrum is also presented for clusters of 25-231 atoms, the largest of which results in the computation of 2310 excited states per sampled cluster geometry.

SIMULATION AND 3D VISUALIZATION OF COMPLEX MOLECULAR STRUCTURE FOR STUDY OF PROTEIN AND NANO MATERIALS

Simulation and visualization of complex bio-molecules are gaining importance; this is because of the fact that functional properties of such molecules are more dependent on their 3D structures. One of the challenges of computational biology is prediction of structures of protein from amino sequence. Three dimensional visualization of molecular structure is also an important research goal in nano engineering. Such visualization, simulation and animation of reaction dynamics are essential for modern chemistry. Force field simulation of large number of atoms in complex molecular structure is computationally challenging. To find equilibrium of force fields and resultant dynamic structure of large atomic clusters which assembles to predictable molecules is one of the major goals of computational biology. In this paper we describe a simple but efficient algorithm (MoliSim3D) to simulate and dynamically visualize in 3D the assembly of atoms in presence of internal and external forces. It helps monitoring and measuring different bond angles, dimensions and displacements of selected portions from thousands of atoms forming target molecule. Pattern recognition, pattern error detection and reaction control are advance tools of virtual molecular assembly. The proposed system is basically intended as educational tool and to help researchers in understanding complex molecular dynamics and functionality with high degree of confidence in simulated environment.

Displacement cascades and defects annealing in tungsten, Part I: Defect database from molecular dynamics simulations

Molecular dynamics simulations have been used to generate a comprehensive database of surviving defects due to displacement cascades in bulk tungsten. Twenty-one data points of primary knock-on atom (PKA) energies ranging from 100eV (sub-threshold energy) to 100keV (∼780×Ed, where Ed=128eV is the average displacement threshold energy) have been completed at 300K, 1025K and 2050K. Within this range of PKA energies, two regimes of power-law energy-dependence of the defect production are observed. A distinct power-law exponent characterizes the number of Frenkel pairs produced within each regime. The two regimes intersect at a transition energy which occurs at approximately 250×Ed. The transition energy also marks the onset of the formation of large self-interstitial atom (SIA) clusters (size 14 or more). The observed defect clustering behavior is asymmetric, with SIA clustering increasing with temperature, while the vacancy clustering decreases. This asymmetry increases with temperature such that at 2050K (∼0.5Tm) practically no large vacancy clusters are formed, meanwhile large SIA clusters appear in all simulations. The implication of such asymmetry on the long-term defect survival and damage accumulation is discussed. In addition, 〈100〉{110} SIA loops are observed to form directly in the highest energy cascades, while vacancy 〈100〉 loops are observed to form at the lowest temperature and highest PKA energies, although the appearance of both the vacancy and SIA loops with Burgers vector of 〈100〉 type is relatively rare.

Can a relativistic differential equation be set up to treat the angularity of the valence electron density in heavy atom clusters?

This work provides an explicit relativistic non-linear differential equation to estimate the ground-state electron density, and especially its directionality dependence, for large clusters of heavy atoms, such as Pb, at their experimentally measured equilibrium geometry. The study embodies the early theory of Vallarta and Rosen, which seems to us to build a firm foundation on relativistic semi-classical many-electron theory. Assuming a finite nuclear radius for the heavy atoms would be advisable in subsequent numerical applications.

Effect of Melt Thermal Treatment on Eutectic Silicon Particles Characteristics in Cast Al-Si-Mg Alloys

A new means of obtaining fine Si particles is through the use of a melt thermal treatment (MTT), where the mixing of low and high temperature alloy melts produces a fine Si structure. Modification is achieved by nuclei resulting from the degeneration of large atom clusters and some refractory solids in the low temperature melt when it is heated by the high temperature melt. This is a relatively recent technique which demonstrates promise as an alternative to Sr-modification, as it requires no element addition, thus reducing the risk of increased porosity normally associated with the addition of strontium to the melt. The use of melt superheat is also found to produce refinement of the eutectic Si structure. In this case, the high melt temperature assists in the degeneration of atom clusters, providing more nuclei for α-Al dendrite formation, and a resulting refinement of the microstructure. KeywordsMelt Thermal Treatment; Melt Superheat; Sr Modification Eutectic Si Particle Characteristics

GPU Computing in XAFS

Modern graphics processing units (GPUs) are powerful parallel computers. Porting the mathematically intense, parallelizable algorithms of XAFS to run on GPUs should expand the scale of tractable XAFS calculations. Part of a time-limiting subroutine in FEFF 8.4 (fms) was converted to run on a GPU, showing significant performance gains. With parallel CPUs sharing GPU resources, the runtime of the modules calling fms should accelerate by one or two orders of magnitude versus a single-threaded CPU process (at least for large atomic clusters,). New or existing XAFS algorithms and programs (e.g. FEFF 9) should show similar acceleration when ported to GPUs, as long as they meet certain criteria (outlined in detail).

The Raman Spectra of Nanocomposite Clusters of Atoms in Phosphorous-Selenium Glassy State

We make clusters of atoms of the size of less than 1 nanometer by using the density functional theory and from that we obtain the bond lengths corresponding to the minimum energy configuration. We are able to optimize large clusters of atoms and find the vibrational frequencies for each cluster. This calculation provides us with a method to identify the clusters present in an unknown sample of a glass by comparing the experimental Raman frequency with the calculated value. We start with the experimental values of the Raman frequencies of PSe (Phosphorous-Selenium) glass. We calculate the structural parameters of PSe, P4Se, P2Se2, P4Se5, PSe4, P4Se3 clusters of atoms and tabulate the vibrational frequencies. We compare the calculated values with those measured. In this way we find the clusters of atoms present in the glass. Some times, the same number of atoms can be rearranged in a different symmetry. Hence we learn the symmetries of molecules. We find that certain symmetries are broken due to self-organization in the glassy state.

Tetrahedron dynamics in the icosahedral quasicrystals i-ZnMgSc and i-ZnAgSc and the cubic 1/1-approximant Zn6Sc

A comparison of periodic approximants and their quasicrystalline counterparts offers the opportunity to better understand the structure, physical properties and stabilizing mechanisms of these complex phases. We present a combined experimental and molecular dynamics study of the lattice dynamics of the icosahedral quasicrystals i-ZnMgSc and i-ZnAgSc and compare it to recently published results obtained for the cubic 1/1-approximant Zn6Sc []. Both phases, quasicrystal and approximant, are built up from large atomic clusters which contain a tetrahedral shell at the cluster centre and are packed either quasiperiodically or on a bcc lattice. Using quasielastic neutron scattering and atomic scale simulations, we show that in the quasicrystal the tetrahedra display a dynamics similar to that observed in the 1/1-approximant: the tetrahedra behave as a ‘single molecule’ and reorient dynamically on a timescale of the order of a few ps. The tetrahedra reorientation is accompanied by a large distortion of the surrounding cluster shells which provide a unique dynamical flexibility to the quasicrystal. However, whereas in the 1/1-approximant the tetrahedron reorientation is observed down to Tc = 160 K, where a phase transition takes place, in the quasicrystal the tetrahedron dynamics is gradually freezing from 550 to 300 K, similarly to a glassy system.

Layer-resolved photoelectron diffraction from Si(0 0 1) and GaAs(0 0 1)

Photoelectron diffraction in the layer-resolved mode brings more detailed information about local atomic arrangement than is obtained in the standard mode. This is demonstrated in crystals with diamond and zinc-blende structures, both for unpolarized photon excitation as well as for circularly polarized excitation. The full angular distributions of photoemission intensities are evaluated for large atomic clusters representing ideally truncated surfaces of Si(001) and GaAs(001). Highly structured layer-resolved patterns enable a more detailed understanding of the standard mode outcomes. Photoelectron intensities from atomic layers placed at different depths under the crystal surface provide direct evidence about electron attenuation and its anisotropy in crystals.

Ordering and dynamics of the central tetrahedron in the 1/1 Zn6Sc periodic approximant to quasicrystal

Periodic approximants to quasicrystals offer a unique opportunity to better understand the structure, physical properties and stabilizing mechanisms of their quasicrystal counterparts. We present a detailed study of the order–disorder phase transition occurring at about 160 K in the Zn6Sc cubic approximant to the icosahedral quasicrystal i-MgZnSc. This transition goes along with an anti-parallel ordering of the tetrahedra located at the centres of large atomic clusters, which are packed on a bcc lattice. Single crystal x-ray diffuse scattering shows that the tetrahedra display pre-transitional short range ordering above Tc (Yamada et al 2012 in preparation). Using quasielastic neutron scattering (QENS) we clearly evidence this short range order to be dynamical in nature above Tc. The QENS data are consistent with a model of tetrahedra ‘jumping’ between almost equivalent positions, which is supported by molecular dynamics simulations. This demonstrates a unique dynamical flexibility of the Zn6Sc structure even at room temperature.

Molecular dynamics simulation of surface deformation via Ar+ ion collision process

We have carried out molecular dynamics (MD) simulations of 50 keV accelerated Ar ions, colliding with a Si surface. Using this procedure the amorphous structural region of the Si was found to expand with the progression of the interface region, that lie between the amorphous structure and the crystalline structure, as fluence increased in the depth direction. There has been considerable interest in studying the time development of the behavior of sputtered silicon atoms after being subjected to collisions with the Ar ions. Here, by tracking the atoms in the computational domain, clusters formed during sputtering are classified under various kinds. In this process small cluster of atoms e.g., monomer and dimer, and large cluster of atoms in forms of hillocks are formed where the smaller cluster have their energy higher than that of the large cluster.

Recent advances and perspectives in four-component Dirac–Kohn–Sham calculations

We review recent theoretical and computational advances in the full relativistic four-component Dirac-Kohn-Sham (DKS) approach and its application to the calculation of the electronic structure of chemical systems containing many heavy atoms. We describe our implementation of an all-electron DKS approach based on the use of G-spinor basis sets, Hermite Gaussian functions, state-of-the-art density-fitting techniques and memory distributed parallelism. This approach has enormously extended the applicability of the DKS method, including for example large clusters of heavy atoms, and opens the way for future key developments. We examine the current limitations and future possible applications of the DKS approach, including the implementation of four-current density functionals and real-time propagation schemes. This would make possible to describe molecules in strong fields, accurately accounting for relativistic kinematic effects and spin-orbit coupling.