Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations are key tools in both improving our understanding of a wide variety of biological processes and accelerating the design and optimization of therapeutics for numerous diseases. Computing power and theory have, however, long been insufficient to enable AFE calculations to be routinely applied in early stage drug discovery. One of the major difficulties in performing AFE calculations is the length of time required for calculations to converge to an ensemble average. CPU implementations of MD‐based free energy algorithms can effectively only reach tens of nanoseconds per day for systems on the order of 50,000 atoms, even running on massively parallel supercomputers. Therefore, converged free energy calculations on large numbers of potential lead compounds are often untenable, preventing researchers from gaining crucial insight into molecular recognition, potential druggability and other crucial areas of interest. Graphics Processing Units (GPUs) can help address this. We present here a seamless GPU implementation, within the PMEMD module of the AMBER molecular dynamics package, of thermodynamic integration (TI) capable of reaching speeds of >140 ns/day for a 44,907‐atom system, with accuracy equivalent to the existing CPU implementation in AMBER. The implementation described here is currently part of the AMBER 18 beta code and will be an integral part of the upcoming version 18 release of AMBER. © 2018 Wiley Periodicals, Inc.     

Enantioselective Cross-couplings between Halide Derivatives and Organometallics by Using Iron and Cobalt Catalysts: Formation of C−C Bonds

This review highlights the recent achievements of iron- and cobalt-catalyzed enantioselective cross-couplings of halide derivatives with organometallic reagents for the construction of C-C bonds. Synthetic applications of enantioselective cross-couplings to natural products and biologically active compounds are also covered showing the power of these cross-couplings in organic synthesis.     

针对连续变化法测定络合物稳定常数实验中可能出现的设计缺陷的讨论

连续变化法测定络合物组成和稳定常数是大学化学中的经典学生实验。但针对1：2和1：3的络合反应，实验教科书的设计中可能出现数据点过少也就是溶液配制过少的问题。如果按照要求配制溶液，由于没有完全反应的混合溶液，而其他混合溶液给出的数据又都呈良好的线性，就缺少了用来估算曲线的数据点，结果是，将没有足够的数据对稳定常数进行估算。对这种可能出现的数据点过少的实验设计的原因、结果和解决方法进行了探讨。     

Development and assessment of an intrusive polynomial chaos expansion-based continuous adjoint method for shape optimization under uncertainties

This article contributes to the development of methods for shape optimization under uncertainties, associated with the flow conditions, based on intrusive Polynomial Chaos Expansion (iPCE) and continuous adjoint. The iPCE to the Navier–Stokes equations for laminar flows of incompressible fluids is developed to compute statistical moments of the Quantity of Interest which are, then, compared with those obtained through the Monte Carlo method. The optimization is carried out using a continuous adjoint-enabled, gradient-based loop. Two different formulations for the continuous adjoint to the iPCE PDEs are derived, programmed, and verified. Intrusive PCE methods for the computation of the statistical moments require mathematical development, derivation of a new system of governing equations and their numerical solution. The development is presented for a chaos order of two and two uncertain variables and can be used as a guide to those willing to extend this development to a different set of uncertain variables or chaos order. The developed method and software, programmed in OpenFOAM, is applied to two optimization problems pertaining to the flow around isolated airfoils with uncertain farfield conditions.     

Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β‐Hairpins

A popular strategy in the de novo design of stable β‐sheet structures for various biomedical applications is the incorporation of aromatic pairs at the non‐hydrogen‐bonding (NHB) position. However, it is important to explicitly understand how aryl pair packing at the NHB region is coordinated with backbone structural rearrangements, and to delineate the benefits and drawbacks associated with stereopositional choice of dissimilar aromatic pairs. Here, we probe the consequences of flipped Trp/Tyr pairs by using engineered permutants at the NHB position of dodecapeptide β‐hairpins, proximal and distal to the turn. Extensive conformational analysis of these peptides using NMR and CD spectroscopy reveal that a classic Edge‐to‐Face and Face‐to‐Edge geometry at the proximal and distal aromatic pairs, respectively, in YW‐WY, is the most stabilizing. Such a preferred packing geometry in YW‐WY results in a highly twisted β‐sheet backbone, with Trp always providing a ‘Face’ orientation to its dissimilar aromatic partner Tyr. Flipping the proximal and/or distal aromatic pair distorts the ideal T‐shaped geometry, and results in alternate aryl arrangements that can adversely affect strand twist and β‐sheet stability. Our study reveals the existence of a strong stereopositional influence on the packing of dissimilar aromatic pairs. Our findings highlight the importance of modeling physical interaction forces while designing protein and peptide structures for functional applications.     

相关光谱式气体检测系统的光学仿真及优化

依据相关光谱式红外气体传感器检测原理,以系统中红外光与气体反应的气室为研究对象,利用光学设计专用软件Tracepro对理想红外朗伯光源在不同反射镜类型下光源的最佳位置进行了仿真分析;通过建立光路传输系统的数学模型,对气室不同结构尺寸下的光功率输出、以及气室内壁反射率对传感系统性能的影响进行了仿真与优化.在理论模型的基础上,根据仿真结果,确定了最佳气室模型的参数组合.实验结果表明,通过对气室中红外光源的位置、反射镜类型、气室长度等部分进行适当的优化修改后,可使探测器接收信号幅度得到明显提高,将有利于后级电路的信号放大、数模转换等处理过程,从而提高气体浓度检测的灵敏度和精度.     

一类综合评价指数编制路径及案例

综合评价指数是一种广义上的统计指数,在讨论了综合评价指数与一般统计指数不同的基础上,引述了综合评价指数一般编制步骤并详细分析研究了综合评价指数编制过程中的权重确定,提出了基于等权设计思想的加权修正综合评价指数编制方法,最后以甘肃省装备制造产业为例进行了展示.     

Exploratory Analysis for Elemental Characterization of Biomass Residues From Biodiesel Production by Inductively Coupled Plasma Optical Emission Spectrometry

Edible and non-edible seeds with high oil content are used as the main raw material for biodiesel production. The residual biomass (press cake or oil cake) can be used as animal feed, to aggregate value to the biodiesel production cycle. In this work, a microwave-assisted-digestion procedure for elementary determination by inductively coupled plasma optical emission spectrometry (ICP OES) using dilute nitric acid was developed. Inter-laboratorial reference material was used to check the accuracy. A full factorial design in addition to exploratory analysis through principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used to classify the samples: press cakes from castor (Ricinus communis), jatropha (Jatropha curcas), radish (Raphanus sativus), sunflower (Heliantus annus), and coffee (Coffe arabica), according to their similarities.     

Three Short Stories about Hexaarylbenzene–Porphyrin Scaffolds

A feasible two‐step synthesis and characterization of a full series of hexaarylbenzene (HAB) substituted porphyrins and tetrabenzoporphyrins is presented. Key steps represent the microwave‐assisted porphyrin condensation and the statistical Diels–Alder reaction to the desired HAB‐porphyrins. Regarding their applications, they proved to be easily accessible and effective high molecular mass calibrants for (MA)LDI mass spectrometry. The free‐base and zinc(II) porphyrin systems, as well as the respective tetrabenzoporphyrins, demonstrate in solid state experiments strong red‐ and near‐infrared‐light emission and are potentially interesting for the application in “truly organic” light‐emitting devices. Lastly, they represent facile precursors to large polycyclic aromatic hydrocarbon (PAH) substituted porphyrins. We prepared the first tetra‐hexa‐peri‐hexabenzocoronene substituted porphyrin, which represents the largest prepared PAH‐porphyrin conjugate to date.