The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion

READY (REActive DYnamics) is a program for studying reactive dynamic systems using a global potential energy surface (PES) built from previously existing PESs corresponding to each of the most important elementary reactions present in the system. We present an application to the combustion dynamics of a mixture of hydrogen and oxygen using accurate PESs for all the systems involving up to four oxygen and hydrogen atoms. Results at the temperature of 4000 K and pressure of 2 atm are presented and compared with model based on rate constants. Drawbacks and advantages of this approach are discussed and future directions of research are pointed out. © 2014 Wiley Periodicals, Inc.     

Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies

Förster resonance energy transfer (FRET) measurements are widely used to investigate (bio)molecular interactions or/and association. FRET efficiencies, the primary data obtained from this method, give, in combination with the common assumption of isotropic chromophore orientation, detailed insight into the lengthscale of molecular phenomena. This study illustrates the application of a FRET efficiency restraint during classical atomistic molecular dynamics simulations of a mutant mastoparan X peptide in either water or 7 M aqueous urea. The restraint forces acting on the donor and acceptor chromophores ensure that the sampled peptide configurational ensemble satisfies the experimental primary data by modifying interchromophore separation and chromophore transition dipole moment orientations. By means of a conformational cluster analysis, it is seen that indeed different configurational ensembles may be sampled without and with application of the restraint. In particular, while the FRET efficiency and interchromophore distances monitored in an unrestrained simulation may differ from the experimentally‐determined values, they can be brought in agreement with experimental data through usage of the FRET efficiency restraining potential. Furthermore, the present results suggest that the assumption of isotropic chromophore orientation is not always justified. The FRET efficiency restraint allows the generation of configurational ensembles that may not be accessible with unrestrained simulations, and thereby supports a meaningful interpretation of experimental FRET results in terms of the underlying molecular degrees of freedom. Thus, it offers an additional tool to connect the realms of computer and wet‐lab experimentation. © 2014 Wiley Periodicals, Inc.     

TiS2 and ZrS2 single‐ and double‐wall nanotubes: First‐principles study

Hybrid density functional theory has been applied for investigations of the electronic and atomic structure of bulk phases, nanolayers, and nanotubes based on titanium and zirconium disulfides. Calculations have been performed on the basis of the localized atomic functions by means of the CRYSTAL‐2009 computer code. The full optimization of all atomic positions in the regarded systems has been made to study the atomic relaxation and to determine the most favorable structures. The different layered and isotropic bulk phases have been considered as the possible precursors of the nanotubes. Calculations on single‐walled TiS₂ and ZrS₂ nanotubes confirmed that the nanotubes obtained by rolling up the hexagonal crystalline layers with octahedral 1T morphology are the most stable. The strain energy of TiS₂ and ZrS₂ nanotubes is small, does not depend on the tube chirality, and approximately obeys to D^–2 law (D is nanotube diameter) of the classical elasticity theory. It is greater than the strain energy of the similar TiO₂ and ZrO₂ nanotubes; however, the formation energy of the disulfide nanotubes is considerably less than the formation energy of the dioxide nanotubes. The distance and interaction energy between the single‐wall components of the double‐wall nanotubes is proved to be close to the distance and interaction energy between layers in the layered crystals. Analysis of the relaxed nanotube shape using radial coordinate of the metal atoms demonstrates a small but noticeable deviation from completely cylindrical cross‐section of the external walls in the armchair‐like double‐wall nanotubes. © 2013 Wiley Periodicals, Inc.     

Developing Thermodynamic Micellization Approach to Model Asphaltene Precipitation Behavior

An little known yet significant issue in petroleum production processes in petroleum reservoirs is asphaltene precipitation/deposition. Asphaltene has not only a fuzzy and vague nature but it also can cause detrimental problems like reservoir blockage and, as a result, low oil recovery. To tackle this issue, many researchers have attempted to monitor asphaltene behavior versus thermodynamic conditions. A thermodynamic micellization approach is implemented in this work to describe asphaltene precipitation behavior for two sample fluids from Iranian reservoirs. First, the basic structures of the addressed approach and different contributions to Gibbs free energy of micellization proposed by Victorov and Firoozabadi (VF) are demonstrated. Second, a detailed sensitivity analysis with respect to the model parameters is performed by utilizing a new calculation strategy. Finally, a comparison between the predicted precipitation curve and the experimental one is illustrated; moreover, comparing our results with those reported by Victorov proves the superiority of the new strategy over the conventional one. The significance of this study shows the effect of each micellization parameter on the asphaltene precipitation behavior curve and illustrates the ability of the micellization approach evolved by VF in monitoring the effect of pressure on asphaltene precipitation using the new calculation procedure. Outcomes from this study could couple with commercial reservoir simulation software to improve precision and integrity for designing robust and effective production units.     

Pairwise decomposition of an MMGBSA energy function for computational protein design

Computational protein design (CPD) aims at predicting new proteins or modifying existing ones. The computational challenge is huge as it requires exploring an enormous sequence and conformation space. The difficulty can be reduced by considering a fixed backbone and a discrete set of sidechain conformations. Another common strategy consists in precalculating a pairwise energy matrix, from which the energy of any sequence/conformation can be quickly obtained. In this work, we examine the pairwise decomposition of protein MMGBSA energy functions from a general theoretical perspective, and an implementation proposed earlier for CPD. It includes a Generalized Born term, whose many‐body character is overcome using an effective dielectric environment, and a Surface Area term, for which we present an improved pairwise decomposition. A detailed evaluation of the error introduced by the decomposition on the different energy components is performed. We show that the error remains reasonable, compared to other uncertainties. © 2014 Wiley Periodicals, Inc.     

铱(Ir~Ⅲ)-稀土(Ln~Ⅲ)异核配合物发光性能研究

稀土离子(LnⅢ)丰富的4f电子跃迁能级,使稀土发光材料获得重要而广泛的应用.稀土配合物中天线基团的引入,弥补了稀土离子f-f跃迁禁阻而导致吸收较低的不足.而具有三重态吸收的过渡金属配合物作为天线基团,更使稀土离子的激发窗口红移.相关研究具有重要的理论意义和实际应用价值.本文主要综述近年来有关铱(IrⅢ)-稀土(LnⅢ)异核发光配合物方面的研究进展.     

Flame Spray Pyrolysis for Finding Multicomponent Nanomaterials with Superior Electrochemical Properties in the CoOx‐FeOx System for Use in Lithium‐Ion Batteries

High‐temperature flame spray pyrolysis is employed for finding highly efficient nanomaterials for use in lithium‐ion batteries. CoO_x‐FeO_x nanopowders with various compositions are prepared by one‐pot high‐temperature flame spray pyrolysis. The Co and Fe components are uniformly distributed over the CoO_x‐FeO_x composite powders, irrespective of the Co/Fe mole ratio. The Co‐rich CoO_x‐FeO_x composite powders with Co/Fe mole ratios of 3:1 and 2:1 have mixed crystal structures with CoFe₂O₄ and Co₃O₄ phases. However, Co‐substituted magnetite composite powders prepared from spray solutions with Co and Fe components in mole ratios of 1:3, 1:2, and 1:1 have a single phase. Multicomponent CoO_x‐FeO_x powders with a Co/Fe mole ratio of 2:1 and a mixed crystal structure with Co₃O₄ and CoFe₂O₄ phases show high initial capacities and good cycling performance. The stable reversible discharge capacities of the composite powders with a Co/Fe mole ratio of 2:1 decrease from 1165 to 820 mA h g^?1 as the current density is increased from 500 to 5000 mA g^?1; however, the discharge capacity again increases to 1310 mA h g^?1 as the current density is restored to 500 mA g^?1.     

Nano-crystalline FeOOH mixed with SWNT matrix as a superior anode material for lithium batteries

Nano-crystalline FeOOH particles(5～10 nm) have been uniformly mixed with electric matrix of single-walled carbon nanotubes(SWNTs)for forming FeOOH/SWNT composite via a facile ultrasonication method. Directly using the FeOOH/SWNT composite(containing 15 wt%SWNTs) as anode material for lithium battery enhances kinetics of the Li+insertion/extraction processes, thereby effectively improving reversible capacity and cycle performance, which delivers a high reversible capacity of 758 mAh g-1under a current density of 400 mA g-1even after 180 cycles, being comparable with previous reports in terms of electrochemical performance for FeOOH anode. The good electrochemical performance should be ascribed to the small particle size and nano-crystalline of FeOOH, as well as the good electronic conductivity of SWNT matrix.     

An energy‐efficient utility‐based distributed data routing scheme for heterogenous sensor networks

A utility‐based distributed data routing algorithm is proposed and evaluated for heterogeneous wireless sensor networks. It is energy efficient and is based on a game‐theoretic heuristic load‐balancing approach. It runs on a hierarchical graph arranged as a tree with parents and children. Sensor nodes are considered heterogeneous in terms of their generated traffic, residual energy and data transmission rate and the bandwidth they provide to their children for communication. The proposed method generates a data routing tree in which child nodes are joined to parent nodes in an energy‐efficient way. The principles of the Stackelberg game, in which parents as leaders and children as followers, are used to support the distributive nature of sensor networks. In this context, parents behave cooperatively and help other parents to adjust their loads, while children act selfishly. Simulation results indicate the proposed method can produce on average more load‐balanced trees, resulting in over 30% longer network lifetime compared with the cumulative algorithm proposed in the literature. Copyright © 2014 John Wiley & Sons, Ltd.