关键词： Cas2   nuclease activity   structure and dynamics  

摘要： Cas2 protein in the CRISPR-Cas system functions as a scaffold for the acquisition of foreign DNA fragments, and as a nuclease against DNA and RNA substrates. Crystal structures of Cas2 have shown catalytically inactive conformational states that do not explain the mechanism of Cas2 nuclease activity. Here, we report that Xanthomonas albilineans Cas2 (XaCas2) assumes an inactive conformation in solution. Residual dipolar couplings and NMR relaxation, however, provide direct evidence on conformational dynamics at the predicted hinge region. Furthermore, XaCas2 transiently associates with metal ions for nuclease activity via highly mobile Asp8. Taken together, the dual function of Cas2 can be explained by a dynamic equilibrium of conformational states that serve as a scaffold or as a nuclease on demand.

关键词： Low-complexity tracking   High-order nonlinear systems   Unknown nonlinearities   Underactuated mechanical systems  

摘要： This paper presents a low-complexity design approach with predefined transient and steady-state tracking performance for global practical tracking of uncertain high-order nonlinear systems. It is assumed that all nonlinearities and their bounding functions are unknown and the reference signal is time varying. A simple output tracking scheme consisting of nonlinearly transformed errors and positive design parameters is presented in the presence of virtual and actual control variables with high powers where the error transformation technique using time-varying performance functions is employed. Contrary to the existing results using known nonlinear bounding functions of model nonlinearities, the proposed tracking scheme can be implemented without using nonlinear bounding functions (i.e., the feedback domination design), any adaptive and function approximation techniques for estimating unknown nonlinearities. It is shown that the tracking performance of the proposed control system is ensured within preassigned bounds, regardless of high-power virtual and actual control variables. The motion tracking problem of an underactuated unstable mechanical system with unknown model parameters and nonlinearities is considered as a practical application, and simulation results are provided to show the effectiveness of the proposed theoretical result.

关键词： Biofilm   Cleaning-in-place   Two-phase kinetics   Wall shear stress   Chemical action   Removal  

摘要： The objective of this study was to investigate the roles of mechanical and chemical actions on the detachment kinetics during CIP of biofilms of Pseudomonas fluorescens at a pilot-plant scale. Biofilms were grown 48 h at 20 degrees C in diluted milk. Shear stress conditions ranged from 0 (static) to 20 Pa and NaOH concentrations from 0.1 to 0.5% w/w. A simple two-phase model was applied to model the removal kinetics and compare detachment parameters. A quick removal of the biofilm during the first phase (4-5 log decrease in three minutes) was followed by a second phase of slow removal of the cells and small aggregates still present at the surface (0-2 log decrease). Hydrodynamics was responsible for removal of both biofilm and single cells while chemicals mainly disrupted biofilm clusters during the first phase. No complete biofilm removal was observed, suggesting a significant role of the interaction forces between bacteria and substrata in the CIP efficiency. (C) 2017 Elsevier Ltd. All rights reserved.

关键词： siRNA   Polyethylenimine   Polymeric nanoparticle   Heparin   Glycosaminoglycan   Polynucleotide delivery   Molecular dynamics  

摘要： Delivery of polynucleotide-based therapeutics into target cells involves interactions with glycoSaminoglycan chains that are located on cell membrane milieu. Mechanisms governing glycosaminoglycan-mediated changes in the nanoparticulate structures of polymer-polynucleotide complexes are unknown, and cannot be fully elucidated without atomistic level details of molecular interactions. We selected a representative nanoparticulate system consisting of a short interfering RNA (siRNA)-poly-ethylenimine complex, and performed all-atom molecular dynamics simulations with the prototypical glycosaminoglycan heparin. We monitored the binding between the complex constituents and the heparin, and identified key features contributing to the response of the siRNA nanoparticles to heparin. We observed three main metastable states that the siRNA nanoparticles might visit in the presence of heparin, which can be translated into different functional outcomes. By correlating our data with the widely different and seemingly contradictory roles previously assigned to glycosaminoglycans, this study provides unique insights into the discrepancies in the experimental literature concerning the role of glycosaminoglycans in the polymeric nanoparticle delivery. (C) 2017 Elsevier Ltd. All rights reserved.

关键词： multilayer network   dynamics   rheological quantities   fluorescence depolarization   generalized Gaussian structures  

摘要： In this paper, we focus on the mechanical relaxation of a multilayer polymer network built by connecting identical layers that have, as underlying topologies, the dual Sierpinski gasket and the regular dendrimer. Additionally, we analyze the dynamics of dipolar energy transfer over a system of chromophores arranged in the form of a multilayer network. Both dynamical processes are studied in the framework of the generalized Gaussian structure (GSS) model. We develop a method whereby the whole eigenvalue spectrum of the connectivity matrix of the multilayer network can be determined iteratively, thereby rendering possible the analysis of the dynamics of networks consisting of a large number of layers. This fact allows us to study in detail the crossover from layer-like behavior to chain-like behavior. Remarkably, we highlight the existence of two bulk-like behaviors. The theoretical findings with respect to the decomposition of the intermediate domain of the relaxation quantities, as well as the chain-like behavior, are well supported by experimental results.

关键词： Nanoindentation   Geopolymer   Molecular dynamics   Indentation size effect  

摘要： Using molecular dynamics simulations, the mechanical response of amorphous geopolymer binder (GB) under spherical nanoindentation was examined as a function of GB composition (Si/Al ratio), indenter size (radius of indenter) and loading rates. The observed hardness values were strongly dependent on the indenter size and loading rates. Specifically, the GB hardness increased with decreasing indenter size and increasing loading-rate. The indenter size effect and the effect of loading rate were related to the ease of rotation of the underlying Si and Al tetrahedra in conjunction with the breaking of bridging Si-O and Al-O bonds. Further, for a given indenter size, increasing the Si/Al ratio increased the hardness and Young's modulus of the GB, which was correlated to higher strength of Si-O bonds as compared to Al-O bonds present in the GB. (C) 2017 Elsevier B.V. All rights reserved.

关键词： Two-dimensional silicon dioxide   Crystalline   Vitreous   Elastic property   Fracture mechanism  

摘要： The recently discovered two-dimensional (2D) silica films can be grown in both crystalline phase and vitreous phase. Using molecular dynamics simulations, we show that these two phases of 2D silica possess vastly different mechanical properties. It is shown that the Young's modulus of crystalline 2D silica is 54% greater than that of its vitreous counterpart. The vitreous 2D silica fails via the ductile fracture with serrated stress-strain curves, while its crystalline counterpart exhibits the abrupt brittle rupture. Both the fracture strength and fracture strain of crystalline 2D silica are significantly larger than those of its vitreous counterpart. Fracture mechanics theory is utilized to give some explanations to the different fracture properties of these two phases. Moreover, 2D silica mixed by crystalline phase and vitreous phase is also studied. Owing to the different mechanical properties of crystalline and vitreous phases, the elastic and fracture properties of this mixed-phase 2D silica are strongly dependent on its crystallinity. Specifically, we find that the Young's modulus of the mixed-phase 2D silica, ranging between the values of its crystalline and vitreous counterparts, increases as the degree of crystallinity increases. Meanwhile, with the increase of the degree of crystallinity the fracture strain of the mixed-phase 2D silica is found to decrease, making its value smaller than that of the purely crystalline and vitreous 2D silica. (C) 2017 Elsevier B.V. All rights reserved.

关键词： Organic-inorganic nanostructures   Self-assembly   Surface assembly  

摘要： Although 'active' surfactants, which are responsive to individual external stimuli such as temperature(1), electric(2,3) or magnetic(4) fields, light(5,6), redox processes(6,7) or chemical agents(8), are well known, it would be interesting to combine several of these properties within one surfactant species. Such multi-responsive surfactants could provide ways of manipulating individual droplets and possibly assembling them into larger systems of dynamic reactors(9,10). Here we describe surfactants based on functionalized nanoparticle dimers that combine all of these and several other characteristics. These surfactants and therefore the droplets that they cover are simultaneously addressable by magnetic, optical and electric fields. As a result, the surfactant-covered droplets can be assembled into various hierarchical structures, including dynamic ones, in which light powers the rapid rotation of the droplets. Such rotating droplets can transfer mechanical torques to their non-nearest neighbours, thus acting like systems of mechanical gears. Furthermore, droplets of different types can be merged by applying electric fields and, owing to interfacial jamming(11,12), can form complex, non-spherical, 'patchy' structures with different surface regions covered with different surfactants. In systems of droplets that carry different chemicals, combinations of multiple stimuli can be used to control the orientations of the droplets, inter-droplet transport, mixing of contents and, ultimately, sequences of chemical reactions. Overall, the multi-responsive active surfactants that we describe provide an unprecedented level of flexibility with which liquid droplets can be manipulated, assembled and reacted.

摘要： In the current paper, we report the kinetics of bifunctional dinuclear platinum(II) complexes viz., 1,2-N, N '-di-(2,2-dipyridylamine)ethanetetraaquaplatinum(II), PtL2, 1,3-N, N '-di-(2,2-dipyridylamine) propanetetraaquaplatinum(II), PtL3, 1,4-N, N '-di-(2,2-dipyridylamine) butanetetraaquaplatinum(II), PtL4, 1,5-N, N ' di-(2,2-dipyridylamine) pentanetetraaquaplatinum(II), PtL5 and 1,6-N, N '-di-(2,2-dipyridylamine) hexanetetraaquaplatinum(II), PtL6. The substitution reactions were carried out on tetraaqua complexes with thiourea nucleophiles under pseudo-first-order conditions as a function of nucleophile concentration and temperature by stopped-flow and UV-vis spectrophotometric techniques. An experimental study was conducted with the aim of determining the influence of alkyl chains on the steric and electronic structure of dinuclear platinum(II) complexes. The reactivity of these complexes was dependent on the length of the alkyl spacer. The results obtained herein demonstrate the intriguing odd-even effects induced by the alkyl chain on the complexes. Artificial constraints imposed by the alkyl chain significantly affect their conformational structure to be either synperiplanar (syn-) or antiperiplanar (anti-) characterized by the odd and even effect. The kinetic, mechanistic and conformational behaviour was influenced by the size of the alkyl chain in accordance with odd-even alterations of the spacer. Computational modeling using density functional theory (DFT) calculations supplemented experimental findings that structural features and the reactivity pattern of these organometallic complexes are governed by both steric and electronic effects arising from the flexibility and inductive nature of the alkyl spacer. The strong s-donicity of longer alkyl chains favours sufficient accumulation of electron density at the metal centre and stabilizes a 14-electron intermediate. The study shows the HOMO-LUMO energy (DE) is affected by the length of the spacer. Kinetic an

关键词： Nucleic acids   Central nervous system   Electrodes   Membranes   Electrodeposition  

摘要： Hydrogen peroxide (H2O2) is an endogenous molecule that plays several important roles in brain function: it is generated in cellular respiration, serves as a modulator of dopaminergic signaling, and its presence can indicate the upstream production of more aggressive reactive oxygen species (ROS). H2O2 has been implicated in, several neurodegenerative diseases, including Parkinson's disease (PD), creating a critical need to identify mechanisms by which H2O2 modulates cellular processes in general and how it affects the dopaminergic nigrostriatal pathway, in particular. Furthermore, there is broad interest in selective electrochemical quantification of H2O2, because it is often enzymatically generated at biosensors as a reporter for the presence of nonelectroactive target molecules. H2O2 fluctuations can be monitored in real time using fast-scan cyclic voltammetry (FSCV) coupled with carbon-fiber microelectrodes. However, selective identification is a critical issue when working in the presence of other molecules that generate similar voltammograms, such as adenosine and histamine. We have addressed this problem by fabricating a robust, H2O2-selective electrode. 1,3-Phenylenediamine (mPD) was electrodeposited on a carbon-fiber microelectrode to create a size-exclusion membrane, rendering the electrode sensitive to H2O2 fluctuations and pH shifts but not to other commonly studied neurochemicals. The electrodes are described and characterized herein. The data demonstrate that this technology can be used to ensure the selective detection of H2O2, enabling confident characterization of the role this molecule plays in normal physiological function as well as in the progression of PD and other neuropathies involving oxidative stress.