在半金属表面上应力诱导的红荧烯晶态薄膜

报道了在Bi（001）衬底上从第一层开始形成的红荧烯晶体薄膜.随着覆盖度的增加,红荧烯薄膜的结构会发生从自组装到混合相的转变.在混合相中存在着红荧烯的晶体畴和分子自组装形成的畴壁.特别是,我们在这种晶体畴中发现了Kurdjunov-Sachs（KS）转动外延和巨大的压缩应力.随着覆盖度的增加,红荧烯薄膜会按照逐层生长的模式进行,直至第四个分子单层.我们认为,转动外延过程中所产生的巨大压缩应力是导致晶态红荧烯薄膜的形成原因.     

A non-conforming monolithic finite element method for problems of coupled mechanics

In this study, a Lagrange multiplier technique is developed to solve problems of coupled mechanics and is applied to the case of a Newtonian fluid coupled to a quasi-static hyperelastic solid. Based on theoretical developments in [57], an additional Lagrange multiplier is used to weakly impose displacement/velocity continuity as well as equal, but opposite, force. Through this approach, both mesh conformity and kinematic variable interpolation may be selected independently within each mechanical body, allowing for the selection of grid size and interpolation most appropriate for the underlying physics. In addition, the transfer of mechanical energy in the coupled system is proven to be conserved. The fidelity of the technique for coupled fluid–solid mechanics is demonstrated through a series of numerical experiments which examine the construction of the Lagrange multiplier space, stability of the scheme, and show optimal convergence rates. The benefits of non-conformity in multi-physics problems is also highlighted. Finally, the method is applied to a simplified elliptical model of the cardiac left ventricle.     

Phosphoinositide-binding interface proteins involved in shaping cell membranes

The mechanism by which cell and cell membrane shapes are created has long been a subject of great interest. Among the phosphoinositide-binding proteins, a group of proteins that can change the shape of membranes, in addition to the phosphoinositide-binding ability, has been found. These proteins, which contain membrane-deforming domains such as the BAR, EFC/F-BAR, and the IMD/I-BAR domains, led to inward-invaginated tubes or outward protrusions of the membrane, resulting in a variety of membrane shapes. Furthermore, these proteins not only bind to phosphoinositide, but also to the N-WASP/WAVE complex and the actin polymerization machinery, which generates a driving force to shape the membranes.     

A two‐grid fictitious domain method for direct simulation of flows involving non‐interacting particles of a very small size

The full resolution of flows involving particles whose scale is hundreds or thousands of times smaller than the size of the flow domain is a challenging problem. A naive approach would require a tremendous number of degrees of freedom in order to bridge the gap between the two spatial scales involved. The approach used in the present study employs two grids whose grid size fits the two different scales involved, one of them (the micro‐scale grid) being embedded into the other (the macro‐scale grid). Then resolving first the larger scale on the macro‐scale grid, we transfer the so obtained data to the boundary of the micro‐scale grid and solve the smaller size problem. Since the particle is moving throughout the macro‐scale domain, the micro‐scale grid is fixed at the centroid of the moving particle and therefore moves with it. In this study we combine such an approach with a fictitious domain formulation of the problem resulting in a very efficient algorithm that is also easy to implement in an existing CFD code. We validate the method against existing experimental data for a sedimenting sphere, as well as analytical results for motion of an inertia‐less ellipsoid in a shear flow. Finally, we apply the method to the flow of a high aspect ratio ellipsoid in a model of a human lung airway bifurcation. Copyright © 2009 John Wiley & Sons, Ltd.     

A comparison between a collocation and weak implementation of the rigid‐body motion constraint on a particle surface

In this work, we implemented and compared two different methods to impose the rigid‐body motion constraint on a solid particle moving inside a fluid. We consider a fictitious domain method to easily manage the particle motion. As the solid as well as the fluid inertia are neglected, the particle can be discretized through its boundary only. The rigid‐body motion is imposed via Lagrange multipliers on the boundary. In the first method, such constraints are imposed in discrete points on the boundary (collocation), whereas in the second the constraint is imposed in a weak way on elements dividing the particle surface. Two test problems, that is, a spherical and an ellipsoidal particle in a sheared Newtonian fluid, are chosen to compare the methods. In both cases, the analysis is carried out in 2D as well as in 3D. The results show that for the collocation method an optimal number of collocation points exist leading to the smallest error. However, small variations in the optimal value can generate large deviations. In the weak implementation, the error is only mildly affected by the number of elements used to discretize the particle boundary and by the Lagrange multiplier's interpolation space. A further analysis is carried out to study the effect of an approximated integration of weak constraints. A comparison between the two methods showed that the same accuracy can be achieved by using less constraints if the weak discretization is used. Finally, the rigid‐body motion imposed via weak constraints leads to better conditioned linear systems. Copyright © 2009 John Wiley & Sons, Ltd.     

Mesoscopic structure and properties of liquid crystalline mesophase pitch and its transformation into carbon fiber

The history and present state of the art in the chemistry of mesophase pitch, which is an important precursor for carbon fiber and other high-performance industrial carbons, are reviewed relative to their structural properties. The structural concepts in both microscopic and macroscopic views are summarized in terms of the sp(2) carbon hexagonal plane as a basic unit common to graphitic materials, its planar stacking in clusters, and cluster assembly into microdomains and domains, the latter of which reflect the isochromatic unit of optical anisotropy. Such a series of structural units is described in a semiquantitative manner corresponding to the same units of graphitic materials, although the size and stacking height of the hexagonal planes (graphitic sheets) are very different. Mesophase pitch is a liquid crystal material whose basic structural concepts are maintained in the temperature range of 250 to 350 degrees C. The melt flow and thermal properties are related to its micro- and mesoscopic structure. The structure of mesophase-pitch-based carbon fiber of high tensile strength, modulus, and thermal conductivity has been formed through spinning, and has inherited the same structural concepts of mesophase pitch. Stabilization settles the structure in successive heat treatments up to 3000 degrees C. Carbonization and graphitization enable growth of the hexagonal planes and their stacking into units of graphite. Such growth is governed and controlled by the alignment of micro- and mesoscopic structures in the mesophase pitch, which define the derived carbon materials as nanostructural materials. Their properties are controlled by the nanoscopic units that are expected to behave as nanomaterials when appropriately isolated or handled.     

In Silico Prediction,Molecular Docking and Dynamics Studies of Steroidal Alkaloids of Holarrhena pubescens Wall. ex G. Don to Guanylyl Cyclase C: Implications in Designing of Novel Antidiarrheal Therapeutic Strategies

The binding of heat stable enterotoxin (STa) secreted by enterotoxigenic Escherichia coli (ETEC) to the extracellular domain of guanylyl cyclase c (ECD_GC-C) causes activation of a signaling cascade, which ultimately results in watery diarrhea. We carried out this study with the objective of finding ligands that would interfere with the binding of STa on ECD_GC-C. With this view in mind, we tested the biological activity of a alkaloid rich fraction of Holarrhena pubescens against ETEC under in vitro conditions. Since this fraction showed significant antibacterial activity against ETEC, we decided to test the screen binding affinity of nine compounds of steroidal alkaloid type from Holarrhena pubescens against extracellular domain (ECD) by molecular docking and identified three compounds with significant binding energy. Molecular dynamics simulations were performed for all the three lead compounds to establish the stability of their interaction with the target protein. Pharmacokinetics and toxicity profiling of these leads demonstrated that they possessed good drug-like properties. Furthermore, the ability of these leads to inhibit the binding of STa to ECD was evaluated. This was first done by identifying amino acid residues of ECD_GC-C binding to STa by protein–protein docking. The results were matched with our molecular docking results. We report here that holadysenterine, one of the lead compounds that showed a strong affinity for the amino acid residues on ECD_GC-C, also binds to STa. This suggests that holadysenterine has the potential to inhibit binding of STa on ECD and can be considered for future study, involving its validation through in vitro assays and animal model studies.     

Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing

ABSTRACT

Existing data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening.     

Directional Self‐Assembly of Fluorinated Star Block Polymer Thin Films Using Mixed Solvent Vapor Annealing

We demonstrate the directional alignment of perpendicular‐lamellae domains in fluorinated three‐armed star block polymer (BP) thin films using solvent vapor annealing with shear stress. The control of orientation and alignment was accomplished without any substrate surface modification. Additionally, three‐armed star poly(methyl methacrylate‐block‐styrene) [PMMA‐PS] and poly(octafluoropentyl methacrylate‐block‐styrene) were compared to their linear analogues to examine the impact of fluorine content and star architecture on self‐assembled BP feature sizes and interdomain density profiles. X‐ray reflectometry results indicated that the star BP molecular architecture increased the effective polymer segregation strength and could possibly facilitate reduced polymer domain spacings, which are useful in next‐generation nanolithographic applications. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1663–1672     

Synthesis and characterization of segmented liquid crystal poly(azoxy polyester-co-polyoxypropylene)

In this study a series of a segmented copolyester, poly(4,4′-dioxy-2,2′-dimethyl-azoxybenzene dodecanedioyl) (PMABD)-co-polyoxypropylene 400 (POP), was prepared. The chain length of PMABD studied (n) was varied from 7.8-18.2, and that of POP was unchanged. The intrinsic viscosity of the segmented copolyesters was 1.04-1.30, and the number average molecular weight obtained was 2.53 × 10⁴?3.49 × 10⁴ g/mol. The mesophase texture and thermal properties of the segmented copolyesters were measured as functions of n. It was found that the insert of flexible POP between those liquid crystalline domains of PMABD did affect thermotropic properties of PMABD. As the n value was 9.0 and 7.8 (or 7.4 and 8.6% by weight POP) the texture appeared as cholesteric-like oily streaks. The effect could not be attained by simply copolymerizing a mesogenic moiety with a pair of spacers of different lengths. The fluidity and domain structure of the flexible dodecanedioyl-POP-dodcanedioyl segments are taken into account for the obtained results. © 1995 John Wiley & Sons, Inc.