Computational combinatorial ligand design: Application to human α-thrombin

Summary A new method is presented for computer-aided ligand design by combinatorial selection of fragments that bind favorably to a macromolecular target of known three-dimensional structure. Firstly, the multiple-copy simultaneous-search procedure (MCSS) is used to exhaustively search for optimal positions and orientations of functional groups on the surface of the macromolecule (enzyme or receptor fragment). The MCSS minima are then sorted according to an approximated binding free energy, whose solvation component is expressed as a sum of separate electrostatic and nonpolar contributions. The electrostatic solvation energy is calculated by the numerical solution of the linearized Poisson-Boltzmann equation, while the nonpolar contribution to the binding free energy is assumed to be proportional to the loss in solvent-accessible surface area. The program developed for computational combinatorial ligand design (CCLD) allows the fast and automatic generation of a multitude of highly diverse compounds, by connecting in a combinatorial fashion the functional groups in their minimized positions. The fragments are linked as two atoms may be either fused, or connected by a covalent bond or a small linker unit. To avoid the combinatorial explosion problem, pruning of the growing ligand is performed according to the average value of the approximated binding free energy of its fragments. The method is illustrated here by constructing candidate ligands for the active site of human -thrombin. The MCSS minima with favorable binding free energy reproduce the interaction patterns of known inhibitors. Starting from these fragments, CCLD generates a set of compounds that are closely related to high-affinity thrombin inhibitors. In addition, putative ligands with novel binding motifs are suggested. Probable implications of the MCSS-CCLD approach for the evolving scenario of drug discovery are discussed.     

静息态脑功能连接在不同认知状态老年人中的应用

目的探讨不同认知状态老年人静息态脑功能连接情况。方法收集阿尔茨海默病患者（AD组）13例、轻度认知功能障碍患者（MCI组）12例、认知正常老年人（对照组）13例，进行磁共振扫描，应用局部一致性（ReHo）方法确定种子点，并进行静息态功能连接分析。结果在静息状态下，AD组和MCI组患者的后扣带回区域、额叶内侧、前额叶背外侧和顶叶部分区域的ReHo均较高。与对照组相比，MCI患者左侧颞叶（颞下回及颞中回）、海马旁回及右侧枕叶舌回、皮层下的部分脑区ReHo显著降低；而右侧额叶（额上回、额中回及中央前回）、顶上小叶及左侧梭状回、颞上回、额下回的部分脑区ReHo显著增高。AD患者变化更加明显，额叶-顶叶，颞叶-脑岛，颞叶-枕叶之间的长距离连接降低，但是额叶内部和枕颞间、丘脑及颞叶间的功能连接增高，3组间差异有统计学意义（P＜0.05）。结论3组不同认知状态老年人的功能连接不同，有助于AD、MCI患者及正常老年人的鉴别诊断。     

Efficient stochastic FEM for flow in heterogeneous porous media. Part 1: random Gaussian conductivity coefficients

This paper is concerned with the development of efficient iterative methods for solving the linear system of equations arising from stochastic FEMs for single‐phase fluid flow in porous media. It is assumed that the conductivity coefficient varies randomly in space according to some given correlation function and is approximated using a truncated Karhunen–Loève expansion. Distinct discretizations of the deterministic and stochastic spaces are required for implementations of the stochastic FEM. In this paper, the deterministic space is discretized using classical finite elements and the stochastic space using a polynomial chaos expansion. The highly structured linear systems which result from this discretization mean that Krylov subspace iterative solvers are extremely effective. The performance of a range of preconditioned iterative methods is investigated and evaluated in terms of robustness with respect to mesh size and variability of the conductivity coefficient. An efficient symmetric block Gauss–Seidel preconditioner is proposed for problems in which the conductivity coefficient has a large standard deviation.The companion paper, herein, referred to as Part 2, considers the situation in which Gaussian random fields are transformed into lognormal ones by projecting the truncated Karhunen–Loève expansion onto a polynomial chaos basis. This results in a stochastic nonlinear problem because the random fields are represented using polynomial chaos containing terms that are generally nonlinear in the random variables. Copyright © 2013 John Wiley & Sons, Ltd.     

Influence of cell and LC parameters on the dynamics of STN liquid crystal displays

The dynamics of super-twisted nematic (STN) liquid crystal displays have rarely been studied. In this article, the dynamic response of STN is analysed in detail. The evolution of director configuration with time was obtained by solving Ericksen–Leslie hydrodynamic equations. The time varying midlayer tilt angle is presented as a measure of dynamic response. The influence on STN dynamics of cell parameters including pretilt angle, twist angle, cell thickness, and of material parameters including d/p, K ₂₂, K ₃₃, were studied.     

Studies on the electro-optical and the light-scattering properties of PDLC films with the size gradient of the LC droplets

Polymer dispersed liquid crystal (PDLC) films with the size gradient of the LC droplets were prepared based on the epoxy/acrylate hybrid polymer matrix. The ultraviolet (UV) intensity gradient was induced by the UV-absorbing dye over the thickness of the samples. Taking advantage of the difference between the epoxy monomers and acrylate monomers in polymerisation rates and the UV intensity gradient, the gradient distribution of the LC droplet size was formed in PDLC films. The effect of the size gradient of the LC droplets on the electro-optical and the light-scattering properties of PDLC films was investigated. The results showed that due to the size gradient distribution of the LC droplets, PDLC films could exhibit the strong light scattering in the UV-visible-near infrared (VIS-NIR) region. Consequently, it provides a potential approach for modulating NIR light transmittance.     

Amphiphilic gradient copolymers of 2‐methyl‐ and 2‐phenyl‐2‐oxazoline: self‐organization in aqueous media and drug encapsulation

Gradient (or pseudo‐diblock) copolymers were synthesized from 2‐methyl‐2‐oxazoline and 2‐phenyl‐2‐oxazoline monomer mixtures via cationic polymerization. The self‐assembling properties of these biocompatible gradient copolymers in aqueous solutions were investigated, in an effort to use the produced nanostructures as nanocarriers for hydrophobic pharmaceutical molecules. Dynamic and static light scattering as well as AFM measurements showed that the copolymers assemble in different supramolecular nanostructures (spherical micelles, vesicles and aggregates) depending on copolymer composition. Fluorescence spectroscopy studies revealed a microenvironment of unusually high polarity inside the nanostructures. This observation is related partly to the gradient structure of the copolymers. The polymeric nanostructures were stable with time. Their structural properties in different aqueous media—PBS buffer, RPMI solution—simulating conditions used in pharmacological/medicinal studies, have been also investigated and a composition dependent behavior was observed. Finally, the hydrophobic drug indomethacin was successfully encapsulated within the gradient copolymer nanostructures and the properties of the mixed aggregates were studied in respect to the initial copolymer assemblies. The produced aggregates encapsulating indomethacin showed a significant increase of their mass and size compared to original purely polymeric ones. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Two optimal Dai–Liao conjugate gradient methods

Two adaptive choices for the parameter of Dai–Liao conjugate gradient (CG) method are suggested. One of which is obtained by minimizing the distance between search directions of Dai–Liao method and a three-term CG method proposed by Zhang et al. and the other one is obtained by minimizing Frobenius condition number of the search direction matrix. Global convergence analyses are made briefly. Numerical results are reported; they demonstrate effectiveness of the suggested adaptive choices.     

Improvement of moving particle semi‐implicit method for simulation of progressive water waves

Precise simulation of the propagation of surface water waves, especially when involving breaking wave, takes a significant place in computational fluid dynamics. Because of the strong nonlinear properties, the treatment of large surface deformation of free surface flow has always been a challenging work in the development of numerical models. In this paper, the moving particle semi‐implicit (MPS) method, an entirely Lagrangian method, is modified to simulate wave motion in a 2‐D numerical wave flume preferably. In terms of consecutive pressure distribution, a new and simple free surface detection criterion is proposed to enhance the free surface recognition in the MPS method. In addition, a revised gradient model is deduced to diminish the effect of nonuniform particle distribution and then to reduce the numerical wave attenuation occurring in the original MPS model. The applicability and stability of the improved MPS method are firstly demonstrated by the calculation of hydrostatic problem. It is revealed that these modifications are effective to suppress the pressure oscillation, weaken the local particle clustering, and boost the stability of numerical algorithm. It is then applied to investigate the propagation of progressive waves on a flat bed and the wave breaking on a mild slope. Comparisons with the analytical solutions and experimental results indicate that the improved MPS model can give better results about the profiles and heights of surface waves in contrast with the previous MPS models. Copyright © 2017 John Wiley & Sons, Ltd.     

Proteins as functional interlayer in organic field-effect transistor

The paper summarizes and discusses the recent advances of proteins as functional interlayers in organic field-effect transistors (OFETs). Specific focus is given on the proteins integrated into the device structure, either to act as dielectric materials or to perform as the functional interlayer between the dielectric and the organic semiconductor (OSC). The main emphasis is give to the location and the specific effect of protein layers in the structure of OFETs. Besides, the possibility of amyloid serving as useful building blocks for OFET is discussed.