Influence of the electron density on the characteristics of terahertz waves generated under laser–cluster interaction

A theory of generation of terahertz radiation under laser–cluster interaction, developed earlier for an overdense cluster plasma [A. A. Frolov, Plasma Phys. Rep. 42. 637 (2016)], is generalized for the case of arbitrary electron density. The spectral composition of radiation is shown to substantially depend on the density of free electrons in the cluster. For an underdense cluster plasma, there is a sharp peak in the terahertz spectrum at the frequency of the quadrupole mode of a plasma sphere. As the electron density increases to supercritical values, this spectral line vanishes and a broad maximum at the frequency comparable with the reciprocal of the laser pulse duration appears in the spectrum. The dependence of the total energy of terahertz radiation on the density of free electrons is analyzed. The radiation yield is shown to increase significantly under resonance conditions, when the laser frequency is close to the eigenfrequency of the dipole or quadrupole mode of a plasma sphere.     

Coulomb explosion of a heated cluster

Coulomb explosion of a charged, nonuniform, and spherically symmetric cluster with a finite ion temperature is investigated. The spatial distributions of the density and mean velocity of accelerated ions, as well as their energy spectra, are obtained and analyzed as functions of the initial temperature. It is shown that taking into account the finite ion temperature eliminates singularities emerging during a Coulomb explosion of a spatially nonuniform cold cluster due to multistream ion motion that arises after breaking the velocity profile of the cluster ions. The characteristic temperature is found above which the spatial distribution and energy spectrum of the expanding ions become regular.     

On an improved clustering algorithm based on node density for WSN routing protocol

To better collect data in context to balance energy consumption, wireless sensor networks (WSN) need to be divided into clusters. The division of clusters makes the network become a hierarchical organizational structure, which plays the role of balancing the network load and prolonging the life cycle of the system. In clustering routing algorithm, the pros and cons of clustering algorithm directly affect the result of cluster division. In this paper, an algorithm for selecting cluster heads based on node distribution density and allocating remaining nodes is proposed for the defects of cluster head random election and uneven clustering in the traditional LEACH protocol clustering algorithm in WSN. Experiments show that the algorithm can realize the rapid selection of cluster heads and division of clusters, which is effective for node clustering and is conducive to equalizing energy consumption.

     

Spatial relations between shrubs and Prosopis glandulosa canopies

Abstract. Prosopis glandulosa, an arborescent legume, may act as a nurse plant that facilitates the establishment of other woody species. We hypothesized that attenuation of radiant energy and increased soil nutrients beneath P. glandulosa canopies facilitate establishment of subordinate shrubs and shrub cluster development. We determined the spatial distribution pattern of shrubs under P. glandulosa at three locations in southern Texas. Density of Celtis pallida, Zanthoxylum fagara, and total woody plants were comparable among the four cardinal directions at each location, which countered the prediction that shrub density would be greater on the north side of P. glandulosa canopies if attenuation of solar energy was a factor in cluster development. Total woody plant density increased with increasing P. glandulosa basal diameter, canopy radius, and height only at one location. Total woody plant density decreased with increasing total N in the upper 15 cm of soil at two of the three locations. Late in shrub cluster development, extraction of N from the soil and incorporation of N into plant tissue in dense shrub clusters may operate to inhibit further increases in subordinate shrub density.     

Emission of terahertz waves in the interaction of a laser pulse with clusters

A theory of generation of terahertz radiation in the interaction of a femtosecond laser pulse with a spherical cluster is developed for the case in which the density of free electrons in the cluster plasma exceeds the critical value. The spectral, angular, and energy characteristics of the emitted terahertz radiation are investigated, as well as its spatiotemporal structure. It is shown that the directional pattern of radiation has a quadrupole structure and that the emission spectrum has a broad maximum at a frequency nearly equal to the reciprocal of the laser pulse duration. It is found that the total radiated energy depends strongly on the cluster size. Analysis of the spatiotemporal profile of the terahertz signal shows that it has a femtosecond duration and contains only two oscillation cycles.     

Architecture, electronic structure and stability of TM@Ge(n) (TM = Ti, Zr and Hf; n = 1-20) clusters: a density functional modeling

The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized gradient approximation. Different parameters, like, binding energy (BE), embedding energy (EE), energy gap between the highest occupied and lowest unoccupied molecular orbitals (HOMO-LUMO), ionization energy (IP), electron affinity (EA), chemical potential etc. of the energetically stable clusters (ground state cluster) in each size are calculated. From the variation of these parameters with the size of the clusters the most stable cluster within the range of calculation is identified. It is found that the clusters having 20 valence electrons turn out to be relatively more stable in both the neutral and the anionic series. The sharp drop in IP as the valence electron count increases from 20 to 21 in neutral cluster is in agreement with predictions of shell models. To study the vibrational nature of the clusters, IR and Raman spectrum of some selected TM@Ge_n (n = 15,16,17) clusters are also calculated and compared. In the end, relevance of calculated results to the design of Ge-based super-atoms is discussed.     

气孔在四季秋海棠营养器官和繁殖器官上的发育及相关性分析

主要观察了气孔在四季秋海棠营养器官和繁殖器官上的分布和发育情况,并分别对叶片和翅上气孔簇大小、气孔簇密度等指标的相关性进行了研究、结果表明:在叶片的下表皮、雌花和雄花的花被片、苞片、小苞片和翅上有气孔分布,而在茎、花梗上却未见气孔分布.叶片下表皮和翅上气孔通常成簇分布.在叶片的下表皮,气孔簇大小与气孔簇密度呈显著的负相关(P<0.05);气孔簇密度与叶片长度呈极显著的负相关(P<0.01).而翅上的气孔簇密度、气孔簇大小与子房长度无显著相关性(P>0.05).在四季秋海棠中,不同器官表皮的气孔簇大小是不同的,这可能与生理功能的不同有关.     

TOUCHSTONE II: a new approach to ab initio protein structure prediction

We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These procedures are readily automated and are being implemented on a genomic scale.     

Exohedral and endohedral adsorption of alkaline earth cations in BN nanocluster

Adsorption of three alkaline earth cations inside and outside of a B₁₂N₁₂ nano-cage in aqueous medium was investigated using density functional theory. The results obtained are discussed in terms of thermodynamic, geometric, and electronic properties. Based on the calculation of enthalpy changes at 298 K and 1 atm, the adsorption of the considered cations was found to be exothermic outside the cluster while it is endothermic inside. It was also found that the exohedral adsorption favorability of the cluster increases in the series: Ca²⁺?<?Mg²⁺?<<?Be²⁺ with Gibbs free energy changes in the range of ?0.08 to ?1.53 eV at B3LYP/6-31G (d) level of theory. Overall, interaction of the cations with the cluster influences the electronic properties of the cluster through stabilizing the HOMO and LUMO as well as reducing the energy gap between them. However, the electronic properties changed much more in the case of endohedral adsorption in comparison with the exohedral adsorption.     

Dipole Mechanism Generation of Terahertz Waves under Laser-Cluster Interaction

The feasibility of dipole radiation of terahertz waves under the action of a femtosecond laser pulse on a cluster is demonstrated theoretically. It is shown that the dipole mechanism of terahertz radiation generation plays a decisive role in the interaction of a laser pulse with small-size clusters with a sufficiently high electron collision frequency. The dependences of the spectral, angular, energetic, and spatiotemporal characteristics of the terahertz signal on the density of free electrons in the cluster plasma under the conditions in which dipole radiation is dominant are investigated. It is shown that the energy of terahertz radiation is maximal under the resonance conditions, when the laser frequency coincides with the eigenfrequency of a spherical cluster.     

A first-principles study of Ni<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript>Pd<Subscript><Emphasis Type="Italic">n</Emphasis></Subscript> (n = 1 − 5) clusters

A first-principle investigation of structures and properties of Ni _n Pd _n (n=1-5) clusters is presented. For this study, the linear combination of Gaussian-type orbitals auxiliary density functional theory (LCGTO-ADFT) method has been employed. In order to determine the lowest energy structures, several isomers in different spin multiplicities were studied, for each cluster size. Initial structures, for which successive geometry optimization was computed without any constrain, were taken along Born–Oppenheimer molecular dynamics (BOMD) trajectories. To discriminate between minima and transition state structures, harmonic frequency analyses were performed at the optimized structures. Ground state structures, bond lengths, harmonic frequencies, dissociation energy, ionization potential, electron affinity and spin density plots are presented. This work demonstrates, that the Pd atoms prefer to allocate on the surface of the cluster structures whose core is formed by the 3d TM atoms type. Moreover, it has been observed that the ground-state structure spin multiplicity increases as the system size grows. The results of this study contribute to gain insight into how structures and energy properties change with cluster size in bimetallic Pd-based alloys.     

DFT study of water adsorption on lignite molecule surface

High moisture content is a main characteristic of low-rank coal, such as lignite. Numerous oxygen containing functional groups in lignite make it represent some special properties, and these functional groups affect the adsorption mechanisms of water molecules on lignite surface. This study reports some typical water?·?·?·?lignite conformations, along with a detailed analysis of the geometry, electrostatic potential distribution, reduced density gradient of interaction, and interaction energy decomposition. The results show that water molecules tend to aggregate around functional groups, and hydrogen bonds play a dominant role in the interaction. The adsorption energy of water cluster on lignite surface is larger than that of isolated water molecule, a good linear relationship between the interaction distance and adsorption energy of layers has been found. Since water is a polar molecule, the local minima and maxima of electrostatic potential in conformations increase along with more water adsorbing on lignite surface. Reduced density gradient analysis shows that H-bonds, van der Waals interaction, and a little steric make up the interaction between water cluster and lignite molecule. In these studied conformations which mainly are H-bond complexes, electrostatic and exchange repulsion play a dominant role, whereas polarization and dispersion make relatively small contribution to the interaction. Attractive and repulsive interaction both affect the stability of water?·?·?·?lignite conformations.     

Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase; comparisons with methane monooxygenase

A combined broken symmetry density functional and electrostatics approach has been used to examine the active sites of the resting (RNR(ox)) and reduced (RNR(red)) forms of class I type ribonucleotide reductase in the protein and solvent environment. Active site cluster geometries and Heisenberg J values are discussed in the context of the available protein data. The total electrostatic interaction energy in the protein comprises a large reaction field component and a much smaller protein field term, the former suggesting strong dielectric polarization between the cluster and protein-solvent dielectrics; the latter is indicative of a very weak link to the protein environment. Decomposition of the protein field term elucidates the major electrostatic interactions between amino acid residues in the RNR R2 local environment and the active site cluster, enabling an energetic comparison of structurally equivalent residues with a related diiron protein, methane monooxygenase.     

A density functional study of chemical,magnetic and thermodynamic properties of small palladium clusters

Structural, chemical, magnetic and thermodynamic properties of palladium clusters Pd_n with n = 2–11 are studied using density functional methods. The average bond length, entropy, enthalpy and polarisability are observed to increase as the cluster grows in size. The binding energy per atom also increases with cluster size. Stability function and atom addition energy change predict that Pd₄, Pd₆ and Pd₉ are relatively more stable than their neighbouring clusters. Electron affinity, electronegativity and electrophilicity values suggest that larger clusters have stronger tendency to accept electrons, thereby supporting the relative stability of Pd₄ and Pd₆. Chemical hardness is also seen to decrease with cluster size, which suggests that large clusters are more prone to changes in their electronic structure. The magnetic properties of these clusters are reported.     

A density functional theory study on the Ti/P binary cluster ions

Under the framework of density functional theory, an all-electron calculation on the geometrical structures and dissociation channels of Ti/P binary cluster ions has been carried out. The P₂, P₃ and P₄ structures are found to be the relatively stable units in these cluster ions. The lowest energy geometries of these Ti/P binary cluster ions may be constructed by bonding Ti, Ti₂, Ti₃ or Ti₄ unit with one or two relatively stable P₂, P₃ and P₄ units. The most possible dissociation channels of these Ti/P binary cluster ions are the detachment of P₂, P₃ or P₄ fragment. It is well consistent with the photodissociation experimental results.     

Density functional theory study of small nickel clusters

The stable geometries and atomization energies for the clusters Ni _n (n = 2–5) are predicted with all-electron density functional theory (DFT), using the BMK hybrid functional and a Gaussian basis set. Possible isomers and several spin states of these nickel clusters are considered systematically. The ground spin state and the lowest energy isomers are identified for each cluster size. The results are compared to available experimental and other theoretical data. The molecular orbitals of the largest cluster are plotted for all spin states. The relative stabilities of these states are interpreted in terms of superatom orbitals and no-pair bonding.     

Physico-chemical mechanisms of transport by micropinocytosis

Blood plasma proteins adsorption on a capillar endoteliocyte membrane surface can be accompanied by the formation of protein clusters. Their superficial protein density is about 10(16) protein globules per m2. The surface density of free energy of such protein layer in a cluster is estimated according to total energy of individual protein globules hydrophobic contribution, and its value is approximately 5 mJ X m-2. It is identical to local variation quantity of the membrane free energy. An alternation of the free surface energy must lead to the appearance of chemically induced and bending moments and to the membrane distortion accompanied by the caveole forming. The blood hydrostatic pressure in capillar lumen (approximately 33 X 10(2)N X m-2) creates the membrane isotropic tension which is proportional to its value and to caveole radius. The latter according to Laplas' equation closes the caveole into the vesicula with the radius approximately 40 nm. The transport of free vesicula by cytoplasmic currents to the basal surface of an endoteliocyte results in exocytosis (which proceeds approximately 0.1 s) with a release of the vesicula surface free energy (approximately 10(-16) J). The capillar endotelium vesicular transport is the indivisible endocytosis-exocytosis process characterized by "the turnover" of the cell plasmic membrane matter without its loss.     

In quest of an empirical potential for protein structure prediction

Key to successful protein structure prediction is a potential that recognizes the native state from misfolded structures. Recent advances in empirical potentials based on known protein structures include improved reference states for assessing random interactions, sidechain-orientation-dependent pair potentials, potentials for describing secondary or supersecondary structural preferences and, most importantly, optimization protocols that sculpt the energy landscape to enhance the correlation between native-like features and the energy. Improved clustering algorithms that select native-like structures on the basis of cluster density also resulted in greater prediction accuracy. For template-based modeling, these advances allowed improvement in predicted structures relative to their initial template alignments over a wide range of target-template homology. This represents significant progress and suggests applications to proteome-scale structure prediction.     

A theoretical study of spin states in Ni-S<Subscript>4</Subscript> complexes and models of the [NiFe] hydrogenase active site

We have applied density functional theory, using both pure (BP86) and hybrid (B3LYP and B3LYP*) functionals, to investigate structural parameters and reaction energies for nickel(II)-sulfur coordination compounds, as well as for small cluster models of the Ni-SI and Ni-R redox state of [NiFe] hydrogenases. Results obtained investigating experimentally well-characterized complexes show that BP86 is well suited to describe the structural features of this class of compounds. However, the singlet-triplet energy splitting and even the computed ground state are strongly dependent on the applied functional. Results for the cluster models of [NiFe] hydrogenases lead to the conclusion that in the reduced protein structures characterized by X-ray diffraction a hydride bridges the two metal centres. The energy splitting of the singlet and triplet states in Ni-R and Ni-SI models is calculated to be very small and may be overcome at room temperature to allow a spin crossover. Moreover, the relative stability of the Ni-SI and Ni-R structures adopted in the present investigation is fully compatible with their involvement in the reversible heterolytic cleavage of H(2).     

Theoretical studies on the structures,intra- and inter-molecular hydrogen bonding interactions in HNF and HNF–H2O clusters in the gaseous,aqueous and solid phases

Hydrazimium nitroformate ([N₂H₅]⁺[C(NO₂)₃]^? , HNF) is an ionic oxidiser used in solid propellants. Its properties are easily affected by H₂O because of its hygroscopicity. In this article, density functional theory (DFT) and molecular dynamics (MD) were employed to study the isolated HNF molecule and the HNF–H₂O cluster in gas phase and in the aqueous solution. Three stable conformations were obtained for HNF in the gas phase and in the aqueous solution, respectively, and each conformation can form several different HNF–H₂O clusters. Irrespective of whether it is in gas phase or in solution, intramolecular hydrogen bond interactions and other interactions (e.g. the binding energy, the dispersion energy, the second-order perturbation energy and the energy gap between frontier orbitals) of HNF are weaker in the clusters than in the isolated state. The initial decomposition energy of the cluster is lower than that of the isolated HNF molecule in both gaseous and aqueous phases, while the dissociation processes are the same. Molecular dynamic simulations showed that the clustered H₂O elongates and weakens the C–NO₂ bond in the solid HNF–H₂O cluster compared with that in the solid HNF. H₂O reduces and weakens intramolecular N–HΛO bonds too, and O–HΛN is the dominant intermolecular hydrogen bond between HNF and H₂O.