Multiscale molecular dynamics using the matched interface and boundary method

The Poisson-Boltzmann (PB) equation is an established multiscale model for electrostatic analysis of biomolecules and other dielectric systems. PB based molecular dynamics (MD) approach has a potential to tackle large biological systems. Obstacles that hinder the current development of PB based MD methods are concerns in accuracy, stability, efficiency and reliability. The presence of complex solvent-solute interface, geometric singularities and charge singularities leads to challenges in the numerical solution of the PB equation and electrostatic force evaluation in PB based MD methods. Recently, the matched interface and boundary (MIB) method has been utilized to develop the first second order accurate PB solver that is numerically stable in dealing with discontinuous dielectric coefficients, complex geometric singularities and singular source charges. The present work develops the PB based MD approach using the MIB method. New formulation of electrostatic forces is derived to allow the use of sharp molecular surfaces. Accurate reaction field forces are obtained by directly differentiating the electrostatic potential. Dielectric boundary forces are evaluated at the solvent-solute interface using an accurate Cartesian-grid surface integration method. The electrostatic forces located at reentrant surfaces are appropriately assigned to related atoms. Extensive numerical tests are carried out to validate the accuracy and stability of the present electrostatic force calculation. The new PB based MD method is implemented in conjunction with the AMBER package. MIB based MD simulations of biomolecules are demonstrated via a few example systems.     

Resolving band-structure evolution and defect-induced states of single conjugated oligomers by scanning tunneling microscopy and tight-binding calculations

We study single conjugated polyphenylene oligomers consisting of 3n (2 ≤ n ≤ 12) phenyl units by means of cryogenic scanning tunneling microscopy and spectroscopy. The spatially resolved local densities of states reveal a progressive development of a continuous conduction band out of discrete molecular orbitals as the length of the oligomers increases. The experimental results are satisfactorily described by tight-binding calculations which gave a conduction band bandwidth of 4.5 ± 0.2 eV and a band gap of 3.1 ± 0.2 eV for an infinitely long polymer. We observed two types of defects, known as conformational torsional angle misfit and metasite kink. Tight-binding as well as density-functional theory model calculations confirm that both types of defects effectively destroy the delocalization.     

Insights into the binding modes of human β<Subscript>3</Subscript>-adrenergic receptor agonists with ligand-based and receptor-based methods

Agonists of β₃-adrenergic receptor (AR) have been thought as potential drugs for the treatment of obesity, type II diabetes, and overactive bladder. In order to clarify the essential structure–activity relationship and the detailed binding modes of β₃-AR agonists as well as to identify new lead compounds activating β₃-AR, ligand-based and receptor-based methods were applied. The pharmacophore models were developed based on 144 β₃-AR agonists. Meanwhile, the homology model of the β₃-AR was built based on the crystal structure of β₂-AR. The pharmacophore model and the homology model mapped with each other very well, and some important information was obtained from the docking result. For example, agonists formed similar hydrogen-bonding interactions with residues Asp117, Arg315, and Asn332, π–π stacking interaction with residues Phe308, and hydrophobic interactions with residues Val118, Val121, Ala197, Phe198, Ala199, Phe309, and Phe328 of β₃-AR. And the major difference about binding mode from the crystal structures of β₁- and β₂-ARs is the hydrogen-bonding interaction with the residue Arg315, which corresponds to the residue Asn313 of β₁-AR and the residue His296 of β₂-AR, respectively. Our findings may be crucial for the design and development of novel selective and potent β₃-AR agonists.     

A carbon–LiFePO<Subscript>4</Subscript> nanocomposite as high-performance cathode material for lithium-ion batteries

A cathode material of an electrically conducting carbon–LiFePO₄ nanocomposite is synthesized by wet ball milling and spray drying of precursor powders prior to a solid-state reaction. The structural characterization shows that the composite is composed of LiFePO₄ crystals and 4.8 wt.% amorphous carbon. Galvanostatic charge/discharge measurements indicate that the composite exhibits a superior high energy and high cycling stability. This composite delivers a discharge capacity of 159.1 mAh g⁻¹ at 0.1 C, 150.8 mAh g⁻¹ at 1 C, and 140.1 mAh g⁻¹ at 2 C rate. The capacity retention of 99% is achieved after 200 cycles at 2 C. The 18,650 cylindrical batteries are assembled using the composite as cathode materials and demonstrate the capacity of 1,400 mAh and the capacity retention of 97% after 100 cycles at 1 C. These results reveal that the as-prepared LiFePO₄–carbon composite is one of the promising cathode materials for high-performance, advanced lithium-ion batteries directed to the hybrid electric vehicle and pure electric vehicle markets.     

The comparison of ZnO nanowire detectors working under two wavelengths of ultraviolet

Schottky-barrier ultraviolet (UV) detectors based on ZnO-nanowires (NWs) were fabricated with Pt as electrodes in this investigation. The ZnO NWs synthesized by the hydrothermal method were characterized by field-emission scanning electron microscopy (FE-SEM), Raman and PL spectroscopy. Photoelectric properties under 254 and 365 nm UV light were investigated. It is found that the photo-response properties of the devices under 365 nm UV light are better than those under 254 nm UV light, which is further illustrated by light transmission theory, energy-band diagram and absorption spectra. The results demonstrate that ZnO NWs detectors with selectivity to near-UV (NUV) light are promising candidates in photoelectric devices.     

Effects of copper and oxygen vacancies on the ferromagnetism of Mn- and Co-doped Cu2O

The ferromagnetic properties of Mn- and Co-doped Cu₂O with copper and oxygen vacancies (V_Cu and V_O) are studied by first-principles calculations. The results indicate that Mn-doped Cu₂O has an antiferromagnetic state in the near configuration, while it has a ferromagnetic state for the far configuration. On the contrary, Co-doped Cu₂O possess a ferromagnetic state regardless of the distance between the two Co atoms. The observed ferromagnetism can be attributed to the 90° ferromagnetic super-exchange mechanism. The presence of V_O can enhance the ferromagnetism, whereas V_Cudepresses it.     

螺旋线型微秒级高压长脉冲产生器数值模拟

 探索了采用CST软件和PSpice软件进行加速器场分布数值模拟的方法,利用该方法可方便地获取设备内部动态场分布图及动态电压变化规律。针对螺旋线型μs级高压长脉冲产生器系统建立了数值模拟模型,给出了详细的模拟步骤及结果。分析表明,利用场分布模拟方法获取的电压变化规律与电路模拟方法获取的结果是一致的。基于CST模拟方法,可以给出螺旋线及主开关等电气结构的瞬态电场分布,场强增强点主要出现在螺旋带的外沿及金属电极连接处,在介质支撑内部也有较高的场强分布。     

A simple augmented ∊-constraint method for multi-objective mathematical integer programming problems

A simple augmented ?-constraint (SAUGMECON) method is put forward to generate all non-dominated solutions of multi-objective integer programming (MOIP) problems. The SAUGMECON method is a variant of the augmented ?-constraint (AUGMECON) method proposed in 2009 and improved in 2013 by Mavrotas et al. However, with the SAUGMECON method, all non-dominated solutions can be found much more efficiently thanks to our innovations to algorithm acceleration. These innovative acceleration mechanisms include: (1) an extension to the acceleration algorithm with early exit and (2) an addition of an acceleration algorithm with bouncing steps. The same numerical example in Lokman and Köksalan (2012) is used to illustrate workings of the method. Then comparisons of computational performance among the method proposed by  and , the method developed by Lokman and Köksalan (2012) and the SAUGMECON method are made by solving randomly generated general MOIP problem instances as well as special MOIP problem instances such as the MOKP and MOSP problem instances presented in Table 4 in Lokman and Köksalan (2012). The experimental results show that the SAUGMECON method performs the best among these methods. More importantly, the advantage of the SAUGMECON method over the method proposed by Lokman and Köksalan (2012) turns out to be increasingly more prominent as the number of objectives increases.     

Towards a multi-objective performance assessment and optimization model of a two-echelon supply chain using SCOR metrics

This paper aims at multi-objective performance assessment and optimization of a multi-period two-echelon supply chain consisting of a supplier and a manufacturer. On the basis of the assessment system of the supply-chain operations reference model, the supply chain’s performance is investigated with respect to costs, assets, agility, reliability and responsiveness. First, methods to quantify these five performance attributes are put forward. Then a multi-objective mathematical programming model is developed for production decision making of components and products so that the supply chain’s performance frontier formed with Pareto efficient performance values can be achieved. Thereafter a simple augmented \(\epsilon \) -constraint method is proposed for searching for all Pareto efficient solutions of the multi-objective mathematical programming problem. Finally, efficiency of the method is demonstrated with a numerical example and a sensitivity analysis is implemented to reveal effects of capacity expansion on supply chains’ performance.     

Studies on the influence of various experimental conditions on electrochemical generation of ferrate(VI) in NaOH-KOH mixed electrolyte

Ferrate(VI) was prepared by electrooxidation in diaphragm electrolyzer with iron wire gauze as anode and NaOH-KOH mixed solution as electrolyte. The influences of various experimental conditions, such as the volume ratio of NaOH-KOH mixed electrolyte, temperature, current density, passivation of iron anode were investigated on ferrate current efficiency. Due to the low solubility of K₂FeO₄ in concentrated alkaline solution and the passivation of iron wire gauze anode, a highest current efficiency over 90% was obtained at 45°C and at a current density of 5 mA cm⁻² in mixed electrolyte with the volume ratio of NaOH: KOH equal to 6: 4. The result is superior to using NaOH and KOH as electrolyte respectively. In addition, polarization curves, scanning electron microscopy (SEM) and electrochemical impedance spectroscopy (EIS) were employed to further study the effects of synthesis conditions on ferrate(VI) in theory. Published in Russian in Elektrokhimiya, 2009, Vol. 45, No. 7, pp. 853–857. The article is published in the original.