Molecular simulations of lactose-bound and unbound forms of the FaeG adhesin reveal critical amino acids involved in sugar binding

F4 fimbriae are protein filaments found in enterotoxigenic Escherichia coli cells and are implicated in the process of bacterial infection due to their function as bacterial adhesins. These filaments are comprised from several proteins, but the bacterial adhesin FaeG, which is a lactose-binding protein, is the major subunit comprising F4 fimbriae. Crystal structures for three variants of the FaeG protein were recently solved, including the ad variant of FaeG that was crystallized in complex with lactose. However, the dynamics of the FaeG protein bound to lactose have not been explored previously using molecular dynamics simulations. Therefore, in order to study the dynamical interactions between the FaeG ad variant and lactose, we have carried out the first all-atom molecular dynamics simulations of this system. We have also probed the role of crystallographic water molecules on the stability of lactose in the FaeG binding site, and have simulated seven FaeG mutants to probe the influence of amino acid substitutions on the ability of FaeG to bind lactose effectively. Our simulations agree well with experimental results for the influence of mutations on lactose binding, provide dynamical insights into the interactions of FaeG with lactose, and also suggest the possibility of additional regions of the FaeG protein that may act as secondary lactose binding sites.     

Correlation of the dynamics of native human acetylcholinesterase and its inhibited huperzine A counterpart from sub-picoseconds to nanoseconds

It is a long debated question whether catalytic activities of enzymes, which lie on the millisecond timescale, are possibly already reflected in variations in atomic thermal fluctuations on the pico- to nanosecond timescale. To shed light on this puzzle, the enzyme human acetylcholinesterase in its wild-type form and complexed with the inhibitor huperzine A were investigated by various neutron scattering techniques and molecular dynamics simulations. Previous results on elastic neutron scattering at various timescales and simulations suggest that dynamical processes are not affected on average by the presence of the ligand within the considered time ranges between 10 ps and 1 ns. In the work presented here, the focus was laid on quasi-elastic (QENS) and inelastic neutron scattering (INS). These techniques give access to different kinds of individual diffusive motions and to the density of states of collective motions at the sub-picoseconds timescale. Hence, they permit going beyond the first approach of looking at mean square displacements. For both samples, the autocorrelation function was well described by a stretched-exponential function indicating a linkage between the timescales of fast and slow functional relaxation dynamics. The findings of the QENS and INS investigation are discussed in relation to the results of our earlier elastic incoherent neutron scattering and molecular dynamics simulations.     

Key manufacturing capability elements and business performance

The purpose of this research was to extend the recent stream of work in operations strategy on the trade-off and cumulative models of manufacturing capability development. Using results from the 1996 Manufacturing Futures Survey, the paper attempts to test whether pursuing more capabilities (the cumulative model) is reflected in improved return on assets. We consider both industry and country effects. Firms with performance in the upper quartile on a capability are described as 'high' performers and the number of times a firm achieves this level represents the number of capability elements that they have. The results show no evidence of the cumulative model. Quality and delivery capabilities are nevertheless strongly evident. Simply adding more capabilities generally produced no improvement in return on assets. Stepwise regression of ROA on the capabilities produced models with good explanatory power in some countries and industries though not all capabilities loaded. When interactions between capability elements were added to the regression models, results were mixed. In some cases, no interactions loaded, while in others, large increases in adjusted R 2 occurred, particularly in industry models.     

Multisoliton complexes in fiber lasers

The formation of stationary and non-stationary pulse groups is regularly observed in multiple pulse soliton fiber lasers. The environment developed in this study for the flexible investigation of this phenomenon is based on the cavity comprising a semiconductor saturable absorber mirror (SESAM) with complex dynamics of absorption recovery and all-fiber dispersion management. The detailed experimental and theoretical considerations show that multiple pulsing in fiber systems offers numerous embodiments ranging from stationary bound states to chaotic bunches. The pulse interaction through the dispersive waves was found to produce a principal impact on the bound state formation. The stability and transformation of stationary bound states and bunch propagation have been also addressed.     

Coupled population balance–CFD simulation of droplet breakup in a high pressure homogenizer

A framework for a one-way coupling between population balance equation (PBE) and computational fluid dynamics (CFD) for emulsions undergoing breakup in a turbulent flow-regime is implemented in the open-source CFD package OpenFOAM. The PBE is discretized using a volume conservative scheme. This framework was applied to emulsification of food-grade vegetable oil-in-water emulsions in a Niro Soavi high pressure homogenizer (HPH) with different pressure drops and using oils of varying viscosities. Different breakage rate models were implemented, as well as the model of Becker et al. (2014) which is an extension of the Luo and Svendsen (1996) model to account for the dispersed phase viscosity. The Becker et al. (2014) model was found to give better predictions after three consecutive passes, without the need for additional empirically determined parameters. The multi-scale PBE–CFD modelling approach allowed a detailed analysis of the breakup process in the gap and jet of the HPH valve.     

Adaptability of competitive electricity reforms a modular analysis

Among the competitive electricity reforms that have been implemented in Europe and the US for the last 18 years, none has “survived” over several years without major changes. Their changing nature raises the question of their adaptability. Two characteristics of reforms play a key role on their adaptation properties. Firstly, they are “modular” objects in the sense of [Baldwin, C., 2008. Where do transactions come from? Modularity, transactions, and the boundaries of firms. Industrial and Corporate Change 17 (1), 155–195]. Secondly, they are produced in an institutional process which leads to “incomplete” rules and designs [Pistor, K., Xu, C., 2003. Incomplete law. International Law and Politics 35, 931–1013]. We propose a typology of adaptations based on the framework proposed by [Williamson, O.E., 1991. Comparative economic organization: the analysis of discrete structural alternatives. Administrative Science Quarterly 36 (2), 269–296] for contracts: (1) in case of small disturbances, adaptations are realized quasi-automatically, by autonomous decisions of the institutions governing the implementation of reforms; (2) in case of middle-range disturbances, adaption is made by Coasian bargaining; (3) finally, in case of strong disturbances, or when bargaining is not feasible, the adaptation of reforms is in the hands of legislative and executive institutions [North, D.C., 2005. Le processus du développement économique. Editions d’Organisation]. These institutions can reform the reforms [Joskow, P.L., 2006. Introduction to electricity sector liberalization: lessons learned from cross-country studies. In: Sioshansi, F.P. (Ed.), Electricity Market Reform: An International Perspective. Elsevier, Amsterdam, pp. 1–32; Hogan, W.W., 2002. Electricity market restructuring: reforms of reforms. Journal of Regulatory Economics 21, 103–132]. The role of these types of adaptations in each electricity reform is a consequence of the allocation of rights to the regulator, to stakeholders and to legislative and executive institutions.     

基于ADAMS的多管火箭炮动力学仿真分析

基于虚拟样机技术，研究多管火箭炮武器系统加装缓冲装置发射时期的动力学特性。根据火箭炮系统的几何模型简化出适合动力学仿真的物理模型，在ADAMS软件平台下建立系统仿真样机，编制仿真发射程序，对比有无缓冲装置条件下火箭炮系统的俯仰轴和方位轴所受冲击扰动力矩和底座的受力的情况，为多管火箭炮系统的设计和试验提供参考数据，有效缩短火箭炮系统开发周期，节省研制经费。     

分子动力学方法的模拟参数对结果的影响

主要研究了利用分子动力学方法(MD)模拟等离子体与材料表面相互作用过程时分子动力学方法的参数对模拟结果的影响.详细分析了Berendsen热浴的应用时间、耦合强度和模拟时间量(单个轨迹的作用时间、弛豫时间)对模拟结果的影响,结果表明,热浴的应用时间对模拟结果的影响很大,而其它参数对模拟结果没有太大的影响.     

Thermal-conductivity and tensile-properties of BN, SiC and Ge nanotubes

Thermal-conductivity and axial tension of single-wall BN (Boron Nitride), SiC (Silicon Carbide) and Ge (Germanium) nanotubes are simulated through the MD (Molecular Dynamics) method, and the conductivity-temperature and loading-strain curves of the nanotubes are given. According to the obtained results, the differences of the nanotubes in thermal-conductivity and tensile-properties are investigated. The results show that the thermal-conductivity of all the tubes decreases with the increase of temperature and diameter; at the same temperature the BN tube has the best thermal-conductivity, whereas the SiC and Ge tubes have the comparable one; the Ge tube has both the worst anti-deformation and anti-loading capability, the BN tube the best anti-deformation one, and the BN and SiC tubes the comparable anti-loading one.