Medium-sized Clusters Research Articles

Dragonfly: A multi-platform parallel toolbox for MATLAB/Octave

In this paper, we present Dragonfly, a free open-source software toolkit that allows creating a parallel collaboration environment between MATLAB and/or Octave instances, allowing us to have a robust system, which is flexible, transparent and interoperable. Dragonfly can be used under multi-platform (Linux, Windows, Mac) and multi-environment configurations (e.g., MATLAB and/or Octave instances). To distribute the workload, it has a flexible system, where programmers can select the computational resources, create clusters and assign weights to balance properly tasks across the distributed environment (MATLAB and Octave instances machines) with different computational power. These functionalities allow obtaining good performance metrics such as: execution time, scalability and efficiency. Finally, this tool has been tested on different computer systems from standard commodity environments to medium size clusters using a set of applications from different scientific fields. This widespread in-field validation allowed showing good performances not only in speedup but also in efficiency using Dragonfly.

Energy landscape of ZnO clusters and low-density polymorphs

We report on an extensive study of ZnO materials with cagelike motifs in clusters and bulk phases through structural searches using the minima hopping method. A novel putative ground state was discovered for the ${(\mathrm{ZnO})}_{32}$ cluster with a tubelike structure, closely related to the previously reported ${(\mathrm{ZnO})}_{24}$ ground-state cage geometry. Furthermore, the effect of ionization on the geometries and energetic ordering of $({\mathrm{ZnO})}_{n}$ clusters with $n=3--10,12$ was studied by directly sampling the energy landscape of the ionized system. Our results indicate that the transition from ring and planar structures to three-dimensional cages occurs at larger cluster sizes than in the neutral system. Inspired by the bottom-up design philosophy and the predominance of cagelike structures in medium-sized clusters, a search for crystalline ZnO was conducted aimed specifically at low-density polymorphs, resulting in the discovery of 57 novel metastable phases. The voids in these low-density materials closely resemble the hollow cage structures of small $({\mathrm{ZnO})}_{n}/({\mathrm{ZnO})}_{n}^{+}$ clusters with $nl16$. Analogous to clathrate materials, these voids could serve to accommodate guest atoms to tailor the materials properties for various applications.

Partitioning big graph with respect to arbitrary proportions in a streaming manner

Using a single commodity computational node to partition big graph is very difficult. This work studies how to partition a big graph with respect to arbitrary proportions in a streaming manner. To meet diverse requirements of big graph partitioning scenarios, we first devise 3 measurement schemes for measuring the graph vertex count, graph workload, and graph processing time, respectively. These schemes are the bases and prerequisites for big graph partitioning. Due to the difficulty in acquiring full big graph information, we then design 8 streaming heuristics to partitioning a big graph during the process of loading its data from external disks into memory. Each of these heuristics decides where to assign every vertex in the stream based on the information calculated by one of the above 3 schemes. At last, we demonstrate the performance and flexibility of our heuristics in partitioning real and synthetic graph datasets on a medium-sized cluster. The characteristics of arbitrary proportions of our approach makes it have a wide range of applications.

A Fukui function-guided genetic algorithm. Assessment on structural prediction of Sin (n = 12-20) clusters.

Theoretical studies are essential for the structural characterization of clusters, when it comes to rationalize their unique size-dependent properties and composition. However, the rapid growth of local minima on the potential energy surface (PES), with respect to cluster size, makes the candidate identification a challenging undertaking. In this article, we introduce a hybrid strategy to explore the PES of clusters. This proposal involves the use of a biased initial population of a genetic algorithm procedure. Each individual in this population is built by assembling small fragments, according to the best matching of the Fukui function. The performance of a genetic algorithm procedure. The performance of the method is assessed on the PES exploration of medium-sized Sin clusters (n = 12-20). The most relevant results are: (a) the method converges at almost half of the time used by the canonical version of the GA and, (b) in all the studied cases, with the exception of Si13 and Si16 , the method allowed to identify the global minimum (GM) and other important low-lying structures. Additionally, the apparent deficiency of the proposal to identify the GM was corrected when a Si atom, or other low-lying isomers, were considered to build the clusters. © 2017 Wiley Periodicals, Inc.

Fragment Quantum Mechanical Method for Large-Sized Ion-Water Clusters.

Fragmentation methods have been widely studied for computing quantum mechanical (QM) energy of medium-sized water clusters, but less attention has been paid to large-sized ion-water clusters, in which many-body QM interaction is more significant, because of the charge-transfer effect between ions and water molecules. In this study, we utilized electrostatically embedded generalized molecular fractionation (EE-GMF) method for full QM calculation of the large-sized ion-water clusters (up to 15 Na+ and 15 Cl- ions solvated with 119 water molecules). Through systematic validation using different fragment sizes, we show that, by using distance thresholds of 6 Å for both the two-body and three-body QM interactions, the EE-GMF method is capable of providing accurate ground-state energies of large-sized ion-water clusters at different ab initio levels (including HF, B3LYP, M06-2X, and MP2) with significantly reduced computational cost. The deviations of EE-GMF from full system calculations are within a few kcal/mol. The result clearly shows that the calculated energies of the ion-water clusters using EE-GMF are close to converge after the distance thresholds are larger than 6 Å for both the two-body and three-body QM interactions. This study underscores the importance of the three-body interactions in ion-water clusters. The EE-GMF method can also accurately reproduce the relative energy profiles of the ion-water clusters.

Revisit of Sin (n = 21–29) Clusters by Ab Initio Global Search

Using our improved genetic algorithm combined with density functional theory calculations, we perform unbiased global search for the most stable structures of Sin clusters with n = 21–29. A new principal direction crossover operation is introduced to search the prolate structures on the potential energy surface. We confirmed previous results for most sized Sin clusters and find more stable structure at n = 23 and 26. In particular, we find a new endohedral cage structure at Si23, which is 0.4 eV lower in energy than previously reported prolate structure and exhibit a distinct peak on the second order difference of total cluster energy. We discuss the competition between prolate and spherical motifs in the medium-sized Sin clusters in light of binding energy and HOMO–LUMO gap. The transition of structural motif from prolate to near spherical in Sin clusters occurs at n = 26. The outer cages are composed of pentagon, hexagon, quadrangle and heptagon, with one to three interior atoms filled inside the cage. These results establish a more complete picture for the structural evolution of the medium-sized silicon clusters. Average bond lengths and Mayer bond order are also discussed.

Structural stability and growth mechanism of neutral and anionic small carbon clusters: Density functional study

In this contribution, we propose a systematic and accurate theoretical methodology to describe the elementary physical processes occurring in sputtering discharges, generating a carbon-containing plasma in which medium size clusters are growing (Cn, n<10). At this stage, we performed density functional calculations to analyse the energetics of many neutral and anionic carbon clusters configurations. We use a wide range exchange-correlation functional (PBE, PBE0, B3LYP, CAMB3LYP, M06-2X and HSE06) with aug-cc-PVDZ basis sets to study the relative stability between linear and cyclic structures. These results show that this relative stability between both depends on the exchange-correlation corrections. For neutral carbon cluster size n<10, the most stable structures are linear for odd values of n and cyclic for even values. For anions, the most stable geometries remain linear irrespective of the cluster size. In both cases, the free energy per carbon atom increases in function of the size. The same results were found in the literature using B3LYP functional. According to these preliminary results, the Meta hybrid GGA functional M06-2X is chosen to explore the relative stabilities of different neutral and anion clusters configurations of Cn, for n⩽6. Other stable isomers are found. Otherwise inter conversion between the most stable isomers have been performed and the growing process of carbon clusters by addition of C or C2 are also present here. The results show that the C2 is more favourable for anions while there is a competition between C and C2 for neutral clusters.

Serotonin-gated inward currents are three times more frequent in rat hairy skin sensory afferents than in those innervating the skeletal muscle.

Tight whole-cell patch clamp was performed in 191 DiI (1,1′-dioctadecyl-3,3,3′3′-tetramethylindocarbocyanine perchlorate) retrogradely labeled rat sensory afferents from skin shoulders (n = 93) and biceps femoris muscles (n = 98). 5-HT-gated inward currents were evoked with 50-µM serotonin (5-HT; 5-hydroxytryptamine), and their frequency and current densities were compared between skin and skeletal muscle sensory afferents. To evaluate if 5-HT-gated inward currents coexist with other ligand-gated currents, the skin and skeletal muscle sensory afferents were also sequentially exposed to external solution at pH 6.8, ATP (50 µM), and capsaicin (1 µM). 5-HT evoked inward currents in 72% (67 of 93) of hairy skin sensory afferents and in only 24% (24 of 98) of skeletal muscle sensory afferents, and this difference was statistically significant (p < 0.0000, chi-square test). The current densities obtained in hairy skin and skeletal muscle sensory afferents were not significantly different. They were −45.8 ± 7.7 and −32.4 ± 10.5 pA/pF, respectively (mean ± SEM, p < 0.30734). These results indicate that 5-HT-gated inward currents are three times more frequently evoked in small- to medium-sized sensory afferents (25–40 µm) innervating the hairy skin than on those innervating the skeletal muscle. When cells were gathered in two clusters, the difference was four times larger in the small-sized cluster (25–32 µm) and two times larger in the medium-sized cluster (33–40 µm). The results can be explained if the superficial somatic (cutaneous) nociceptive system is more exposed than the deep somatic nociceptive system (musculoskeletal) to physical and chemical stimuli inducing 5-HT-mediated inflammatory pain.

Advances in spectroscopy and dynamics of small and medium sized molecules and clusters.

Investigations of the spectroscopy and dynamics of small- and medium-sized molecules and clusters represent a hot topic in atmospheric chemistry, biology, physics, atto- and femto-chemistry and astrophysics. Nowadays, outstanding developments, both theoretical and experimental, have been achieved. The most recent results of these achievements are reviewed here. These molecular systems are studied by means of high-resolution spectroscopic techniques in either the frequency or the time domains. However, they still represent complex molecular systems since they may undergo processes that are still not fully understood in sufficient details. Indeed, electronic and nuclear motions may lead to complex features that are observed experimentally. From a theoretical point of view, these features can only be interpreted if the quantum nature of the atomic nuclei is considered together with the possible couplings between nuclear and electronic degrees of freedom. New developments, from both theoretical and experimental sides, are needed for modeling and engineering applications of outstanding importance. Possible future research directions are discussed.

Innovative potential in the small and medium-sized enterprises regional clusters in Russia

Accelerated development of small and medium-sized enterprises is necessary for dynamic regional growth. The fastest growth of small and medium-sized enterprises takes place in clusters. However, clusters of small and medium-sized enterprises are usually engaged in the simplest activities, do not implement innovations. The purpose of the article is to identify and evaluate the innovative potential of existing clusters of small and medium-sized enterprises in the regions of Russia. A research method is the comparative analysis, trend and index analysis, case-method, methods of statistical information processing. The study found a low level of innovation activity in clusters of small and medium-sized enterprises. Their impact on the qualitative development of the regional economy is severely limited. The main reason is weak internal innovation potential and lack of integration with innovation generators. Technological entrepreneurship is developing poorly. The size of the cluster of small and medium-sized enterprises is insufficient to form the infrastructure and elements of the innovation system. Innovative institutions can be formally included in the cluster, but there is no real interaction. Consequently, existing clusters of small and medium-sized enterprises solve only a limited number of specific tasks. Objective advantages of the cluster (positive effects of territorial concentration, diffusion of innovations, collective interactions) need to be complemented by elements of a regional innovation system. The development of the innovative potential of clusters of small and medium-sized enterprises requires interaction with the research and development sector, development institutions, the state, and public organizations. In addition, specific support is required for innovative activity of clusters of small and medium-sized enterprises. Under these conditions, clusters of small and medium-sized enterprises can positively affect the quality of economic growth in the territories.

Benchmarking Density Functional Based Tight-Binding for Silver and Gold Materials: From Small Clusters to Bulk.

We benchmark existing and improved self-consistent-charge density functional based tight-binding (SCC-DFTB) parameters for silver and gold clusters as well as for bulk materials. In the former case, our benchmarks focus on both the structural and energetic properties of small-size AgN and AuN clusters (N from 2 to 13), medium-size clusters with N = 20 and 55, and finally larger nanoparticles with N = 147, 309, and 561. For bulk materials, structural, energetics and elastic properties are discussed. We show that SCC-DFTB is quite satisfactory in reproducing essential differences between silver and gold aggregates, in particular their 2D-3D structural transitions, and their dependency upon cluster charge. SCC-DFTB is also in agreement with DFT and experiments in the medium-size regime regarding the energetic ordering of the different low-energy isomers and allows for an overall satisfactory treatment of bulk properties. A consistent convergence between the cohesive energies of the largest investigated nanoparticles and the bulk's is obtained. On the basis of our results for nanoparticles of increasing size, a two-parameter analytical extrapolation of the cohesive energy is proposed. This formula takes into account the reduction of the cohesive energy for undercoordinated surface sites and converges properly to the bulk cohesive energy. Values for the surface sites cohesive energies are also proposed.

Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling.

ABSTRACTPhysiological resistance to antibiotics confounds the treatment of many chronic bacterial infections, motivating researchers to identify novel therapeutic approaches. To do this effectively, an understanding of how microbes survive in vivo is needed. Though much can be inferred from bulk approaches to characterizing complex environments, essential information can be lost if spatial organization is not preserved. Here, we introduce a tissue-clearing technique, termed MiPACT, designed to retain and visualize bacteria with associated proteins and nucleic acids in situ on various spatial scales. By coupling MiPACT with hybridization chain reaction (HCR) to detect rRNA in sputum samples from cystic fibrosis (CF) patients, we demonstrate its ability to survey thousands of bacteria (or bacterial aggregates) over millimeter scales and quantify aggregation of individual species in polymicrobial communities. By analyzing aggregation patterns of four prominent CF pathogens, Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus sp., and Achromobacter xylosoxidans, we demonstrate a spectrum of aggregation states: from mostly single cells (A. xylosoxidans), to medium-sized clusters (S. aureus), to a mixture of single cells and large aggregates (P. aeruginosa and Streptococcus sp.). Furthermore, MiPACT-HCR revealed an intimate interaction between Streptococcus sp. and specific host cells. Lastly, by comparing standard rRNA fluorescence in situ hybridization signals to those from HCR, we found that different populations of S. aureus and A. xylosoxidans grow slowly overall yet exhibit growth rate heterogeneity over hundreds of microns. These results demonstrate the utility of MiPACT-HCR to directly capture the spatial organization and metabolic activity of bacteria in complex systems, such as human sputum.

Structures and magnetic properties of Ni n (n = 36-40) clusters from first-principles calculations

A genetic algorithm (GA) coupled with a tight-binding (TB) interatomic potential is used to search for the low-energy structures of medium-sized Ni n (n = 36-40) clusters. Structural candidates obtained from our GA search are further optimized with first-principles calculations. The medium-sized nickel clusters ranging from 36 to 40 atoms are found to favor the double-icosahedron-based structures with a Ni7 core (a pentagonal bipyramidal structure) except Ni38 cluster. The lowest-energy structure of Ni38 can be considered to be a magic cluster, which is a typical face-centered cubic structure with large stability and magnetic moment.

Application of a Dual-Hybrid Direct Random Phase Approximation to Water Clusters

In water clusters, there is a delicate balance of van der Waals interactions and hydrogen bonds. Although semilocal and nonlocal density functional approximations have been recently routinely applied to water in various phases, the accurate description of hydrogen bonds remains a challenge. The most popular density functional approaches fail to predict the correct ordering of the energies of water clusters. To illustrate the required accuracy, the CCSD(T) complete basis set extrapolated dissociation energy difference between the two lowest energy hexamer structures is 0.06 kcal mol(-1) per monomer. In this work, we assessed interaction energies in neutral and ionic water clusters with various density functionals with or without van der Waals correction. Generally, van der Waals approximations play a significant role in clusters with increasing size, while hybrid functionals improve the description of hydrogen bonds. Despite these general trends, none of the tested density functional approximations with or without van der Waals correction and exact exchange mixing can lead to a uniform performance for neutral and ionic water clusters. The recently constructed dual-hybrid dRPA75 approximation is a successful combination of exact and semilocal exchange, and nonlocal correlation in its energy, while utilizing a high fraction of exact exchange. We have shown that the dRPA75 method has a systematic error, which can be efficiently compensated for by the aug-cc-pVTZ basis set for small- and medium-sized water clusters.

Accurate calculation of binding energies for molecular clusters – Assessment of different models

In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are <1kJ/mol. Since they are smaller than the basis set errors, we obtain higher total accuracy due to the applicability of larger basis sets. The final CCSD(T)/CBS benchmark values are ΔE=-278.01kJ/mol for (H2O)10,ΔE=-221.64kJ/mol for (HF)10,ΔE=-45.63kJ/mol for (CH4)10,ΔE=-19.52kJ/mol for (H2)20 and ΔE=-7.38kJ/mol for (H2)10.Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods.We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)—MP2/TZ we get a mean error of 0.34kJ/mol and a standard deviation of 0.39kJ/mol.

Spectroscopy and Dynamics of Medium-Sized Molecules and Clusters: Theory, Experiment, and Applications.

Spectroscopy and Dynamics of Medium-Sized Molecules and Clusters: Theory, Experiment, and Applications.

Are fragment-based quantum chemistry methods applicable to medium-sized water clusters?

Fragment-based quantum chemistry methods are either based on the many-body expansion or the inclusion-exclusion principle. To compare the applicability of these two categories of methods, we have systematically evaluated the performance of the generalized energy based fragmentation (GEBF) method (J. Phys. Chem. A, 2007, 111, 2193) and the electrostatically embedded many-body (EE-MB) method (J. Chem. Theory Comput., 2007, 3, 46) for medium-sized water clusters (H2O)n (n = 10, 20, 30). Our calculations demonstrate that the GEBF method provides uniformly accurate ground-state energies for 10 low-energy isomers of three water clusters under study at a series of theory levels, while the EE-MB method (with one water molecule as a fragment and without using the cutoff distance) shows a poor convergence for (H2O)20 and (H2O)30 when the basis set contains diffuse functions. Our analysis shows that the neglect of the basis set superposition error for each subsystem has little effect on the accuracy of the GEBF method, but leads to much less accurate results for the EE-MB method. The accuracy of the EE-MB method can be dramatically improved by using an appropriate cutoff distance and using two water molecules as a fragment. For (H2O)30, the average deviation of the EE-MB method truncated up to the three-body level calculated using this strategy (relative to the conventional energies) is about 0.003 hartree at the M06-2X/6-311++G** level, while the deviation of the GEBF method with a similar computational cost is less than 0.001 hartree. The GEBF method is demonstrated to be applicable for electronic structure calculations of water clusters at any basis set.

Growth patterns and structural motifs of cadmium clusters with up to 60 atoms: disordered or not?

Using two different approaches, the structures of Cdn clusters are optimized. At first, parameterized density-functional calculations using the DFTB method in combination with evolutionary algorithms provide one set of candidate structures. Second, earlier proposed structures based on the Gupta potential provide a second set. Subsequently, all structures of each set are re-optimized using parameter-free density-functional calculations. It turned out that those based on the DFTB calculations in almost all cases were those of the lowest total energy. By analysing the structural properties as a function of cluster size information on growth patterns can be extracted. Thereby, the results show a certain preference that the atoms of the inner parts have surroundings as found in bulk hcp Cd. Furthermore, for larger size ranges, we could identify a specific growth pattern, implying that most of these clusters cannot be classified as being disordered. The results show also that the 4d electrons have only a weak influence on the properties of the clusters that, however, is so strong that a jellium-like model occasionally becomes inaccurate in describing the properties. In particular, the question at which size the clusters can be considered to be metallic becomes non-trivial to answer. Further arguments based on a comparison of the HOMO-LUMO gaps with the Kubo gap, however, suggested the non-metallic properties in the studied size range.

Medium-sized phosphorus cluster cations P+ 2m+1 (6 ≤ m ≤ 32) studied by collision-induced dissociation mass spectrometry.

Medium-sized phosphorus cluster cations were generated by laser ablation of red phosphorus and investigated by the method of collision-induced dissociation mass spectrometry. Experimental results show that the primary dissociation channels of phosphorus cluster cations of P(+) 2m+1 (6 ≤ m ≤ 11) are all characterized by the loss of P4 unit. For larger cluster cations, their dissociation pathways were more complex. For those magic cations of P(+) 8k+1 observed previously, their dissociation pathways progressively change from the loss of P4 unit (for k = 3) to the loss of P8 unit (for k = 4, 5). A new dissociation pathway characterized by the loss of P10 unit was also indentified for larger cations of P(+) 8k+1 (6 ≤ k ≤ 8). Theoretical calculation also shows that, for cations of P(+) 2m+1 (4 ≤ m ≤ 10), the dissociation channel characterized by the loss of P4 unit is more energetically favorable than other dissociation channels, which is in good agreement with the experimental results.

Real-time fragmentation dynamics of clusters ionized by intense extreme-ultraviolet pulses

We investigate the fragmentation dynamics of atomic clusters ionized by intense extreme-ultraviolet pulses from a high-order harmonic generation source. It is demonstrated that the transient modification of the trimer fragment yield induced by a weak near-infrared (NIR) probe pulse provides valuable information on the cluster disintegration process. For medium-sized Ar clusters and delays of around 5 ps, we observe a transition from a collective response, where efficient absorption of the NIR laser energy takes place, to a state where the interaction of the probe laser pulse with individual fragments dominates. The cluster disintegration is faster for smaller clusters, in agreement with a simple physical picture taking into account the measured expansion speeds of excited and ionic fragments. For Xe clusters, we find a significantly increased fragmentation time of about 40 ps, attributed to the larger atomic mass and to more efficient electron–ion recombination processes.