关键词： DNA origami   DNA hinges   molecular dynamics simulations   coarse-grained modeling   dynamic nanostructures   compliant mechanisms   conformational fluctuations  

摘要： Structural DNA nanotechnology, the assembly of rigid 3D structures of complex yet precise geometries, has recently been used to design dynamic, mechanically compliant nanostructures with tunable equilibrium conformations and conformational distributions. Here we use coarse-grained molecular dynamics simulations to provide insights into the conformational dynamics of a set of mechanically compliant DNA nanostructures DNA hinges that use single-stranded DNA "springs" to tune the equilibrium conformation of a layered double-stranded DNA "joint" connecting two stiff "arms" constructed from DNA helix bundles. The simulations reproduce the experimentally measured equilibrium angles between hinge arms for a range of hinge designs. The hinges are found to be structurally stable, except for some fraying of the open ends of the DNA helices comprising the hinge arms and some loss of base-pairing interactions in the joint regions coinciding with the crossover junctions, especially in hinges designed to exhibit a small bending angle that exhibit large local stresses resulting in strong kinks in their joints. Principal component analysis reveals that while the hinge dynamics are dominated by bending motion, some twisting and sliding of hinge arms relative to each other also exists. Forced deformation of the hinges reveals distinct bending mechanisms for hinges with short, inextensible springs versus those with longer, more extensible springs. Lastly, we introduce an approach for rapidly predicting equilibrium hinge angles from individual force-deformation behaviors of its single- and double-stranded DNA components. Taken together, these results demonstrate that coarse-grained modeling is a promising approach for designing, predicting, and studying the dynamics of compliant DNA nanostructures, where " conformational fluctuations become important, multiple deformation mechanisms exist, and continuum approaches may not yield accurate properties.

摘要： The plasma membrane proteome plays a crucial role in inter- and intracellular signaling, cell survival, and cell identity. As such, it is a prominent target for pharmacological intervention. The relatively low abundance of this subproteome in conjunction with challenging extractability and solubility still hampers its comprehensive analysis. Here, we combined a chemical glycoprotein-tagging strategy with mass spectrometry to enable comprehensive analysis of the cell-surface glycoproteome. To benchmark this workflow and to provide guidance for cell line selection for functional experiments, we generated an inventory of the N-linked cell-surface glycoproteomes of 15 standard laboratory human cell lines and three primary lymphocytic cell types. On average, about 900 plasma membrane and secreted proteins were identified per experiment, including more than 300 transporters and ion channels. Primary cells displayed distinct expression of surface markers and transporters underpinning the importance of carefully validating model cell lines selected for the study of cell surface-mediated processes. To monitor dynamic changes of the cell-surface proteome in a highly multiplexed experiment, we employed an isobaric mass tag-based chemical labeling strategy. This enabled the time-resolved analysis of plasma membrane protein presentation during differentiation of the monocytic suspension cell line THP-1 into macrophage-like adherent cells. Time-dependent changes observed in membrane protein presentation reflect functional remodeling during the phenotypic transition in three distinct phases: rapid surface presentation and secretion of proteins from intracellular pools concurrent with rapid internalization of no longer needed proteins and finally delayed presentation of newly synthesized macrophage markers. Perturbation of this process using marketed receptor tyrosine kinase inhibitors revealed dasatinib to severely compromise macrophage differentiation due to an off-target activit

摘要： In this work, we investigate the deformation mechanism of auxetic hierarchical rotating square systems through a dynamics approach. We show how their deformation behaviour, hence their mechanical properties and final configuration for a given applied load, can be manipulated solely by altering the resistance to rotational motion of the hinges within the system. This provides enhanced tunability without necessarily changing the geometry of the system, a phenomenon which is not typically observed in other non-hierarchical unimode auxetic systems. This gives this hierarchical system increased versatility and tunability thus making it more amenable to be employed in practical application which may range from smart filtration to smart dressings.

关键词： Polyurethane   Crosslinking   Maturation   Aging   FTIR-ATR spectroscopy   Dielectric spectroscopy   Tensile test  

摘要： Due to their chemical and morphological versatility, polyurethanes may be susceptible to fabrication conditions (curing procedure, moisture). Industry reports 'maturation' phenomena, i.e. unstable mechanical properties of PU elastomers and PU based adhesive joints right after fabrication. This paper elucidates the impact of fabrication conditions and possible causes of maturation. Chemical and physical bulk properties of a crosslinking two-part PU are monitored during and after cure in dry atmosphere (at room temperature followed by a post-cure). The influence of curing procedure is revealed by processes characteristic of the post-cure, i.e. chemical side reactions (allophanate, carbodiimide) and a new dielectric relaxation. Tensile tests demonstrate the practical relevance of the findings (mechanical modulus). Properties of the fully crosslinked, dryly stored PU are stable during a three-week observation, indicating that maturation is preventable by complete cure and dry conditions. In contrast, chemical crosslinking after an insufficient cure likely causes maturation phenomena. (C) 2017 Elsevier Ltd. All rights reserved.

关键词： Silicon   Chemical mechanical polishing   H2O2   ReaxFF   Molecular dynamics simulation  

摘要： ReaxFF reactive molecular dynamics simulations are employed to study the process of the silica abrasive particle sliding on the Si (100) substrate in the aqueous H2O2 in order to clarify the atomistic mechanisms of the Si chemical mechanical polishing (CMP) process. Our results reveal that the mechanical sliding effects induced chemical reactions at the abrasive particle and Si substrate interface dominate the CMP process and lead to the removal of Si atoms. Before the abrasive particle and Si substrate surface interact mechanically, aqueous H2O2 can make the Si substrate more oxidized. Once they contact with each other, they are connected by the interfacial Si-O-Si bridge bonds due to the chemical reactions at the interface. Under the mechanical sliding effects, the Si-Si and Si-O bonds on the Si substrate can be mechanically strained to be broken, leading to the removal of Si atoms from the Si substrate. Compared with the CMP process in pure H2O, the CMP process in the aqueous H2O2 leads to more oxidized substrate and the removal of more Si atoms, demonstrating the significant role of H2O2 as an oxidizer. Besides, the friction force is higher than that in the pure H2O case due to the stronger interfacial covalent bonds formation and breaking. Our results may shed light on the removal mechanism of Si atoms in the CMP process at the atomic level and provide an effective method to help design the components of the CMP slurry. (C) 2017 Elsevier B.V. All rights reserved.

关键词： c-BN   Thin layers   Tension property   Fracture mechanism   Molecular dynamics  

摘要： Molecular dynamics simulations were performed to investigate the axial tension properties and fracture mechanisms of the c-BN nano thin layers. It is found that thin layers display a linear stress-strain relationship firstly at epsilon < 0.054, and then a quasi-linear response at 0.054 < epsilon < 0.302, and finally the stresses decrease gradually until entire fracture occurs. Fracture stresses are 76, 49, 33 and 21 GPa, respectively, for 100 K, 300 K, 500 K and 700 K, and Young's modulus decreases gradually with the increasing of temperature. The deterioration in mechanical properties derives from the formation of major defects that B-N bond, tetragonum and octagon with broken bonds, and two-hexagon by the sharing of the nitrogen atom. The results not only clear the outstanding property of c-BN nano thin layers but also built relevance between the mechanical behaviors and loading conditions such as side length, temperature and strain rates. (C) 2017 Elsevier B.V. All rights reserved.

关键词： SiC/graphene composites   Mechanical properties   Interface structure   Multilayer graphene  

摘要： The mechanical properties of the SiC/graphene composites under tensile are studied via molecular dynamics (MD) methods. In our study, the SiC/graphene composites with monolayer graphene and multilayer graphene are built and compared. As a result, the composites with different interface structures present different tensile behaviors. The single graphene sheet in contact with Si-terminated SiC(111) surface brings the higher failure strain and strength. It is also found that the elastic modulus of the composites increase with the increasing graphene volume fraction. As for the composites fabricated with the multilayers graphene, the failure strain of the whole systems would decrease with the increasing graphene layers in the case that graphene serves as single layer. By contrast, when the graphene sheets serve as continuous layers, the failure strain does not change significantly and the strength would increase monotonically with the increasing number of graphene layers. (C) 2017 Elsevier B.V. All rights reserved.

关键词： Dry reforming   Kinetics   Methane   Perovskite   SmCoO3   Syngas  

摘要： The kinetics of the methane dry (CO2) reforming over the SmCoO3 was investigated in the temperature ranged 973-1073 K by varying the CH4 and CO2 partial pressures. Based on detailed study of the reaction mechanism, a mechanistic model is proposed from which a kinetic model is derived. The mechanistic pattern assumes adsorption of CH4 on reduced Co, followed by methane cracking and carbon deposition. CO2 reacts with Sm2O3 to form Sm2O2CO3 and the oxycarbonates react with carbon to produce CO. The power law and Langmuir Hinshelwood kinetic model which is established on this mechanism were able to forecast the kinetic results. (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.