Tunable Probes with Direct Fluorescence Signals for the Constitutive and Immunoproteasome

Electrophiles are commonly used for the inhibition of proteases. Notably, inhibitors of the proteasome, a central determinant of cellular survival and a target of several FDA‐approved drugs, are mainly characterized by the reactivity of their electrophilic head groups. We aimed to tune the inhibitory strength of peptidic sulfonate esters by varying the leaving groups. Indeed, proteasome inhibition correlated well with the pK_a of the leaving group. The use of fluorophores as leaving groups enabled us to design probes that release a stoichiometric fluorescence signal upon reaction, thereby directly linking proteasome inactivation to the readout. This principle could be applicable to other sulfonyl fluoride based inhibitors and allows the design of sensitive probes for enzymatic studies.     

The completeness of the sines and cosines in the space of integrable functions

The paper addresses the completeness of sines and cosines with non-integer indices in the space of Lebesgue-integrable functions. The criteria for the variation from the integer value have been found such that sine and cosine systems are complete.     

缆机起重作业驾驶员的操作行为可靠性研究

缆机是大坝浇筑过程中的主要运输设备之一,缆机驾驶员操作水平直接关系缆机起重作业安全.为有效提高缆机起重作业驾驶员操作行为可靠性,预防起重作业安全事故,针对缆机起重作业周期性多维运动的特点,分解驾驶员操作流程;剖析操作行为失误,建立驾驶员行为模式;从时间角度量化操作流程,计算缆机驾驶员操作行为响应失误概率;构建操作行为可靠性分析模型,定量表达操作行为可靠性,分析人因失误对缆机起重作业安全事故的影响.结果表明,吊具与吊罐对接、混凝土卸料等作业过程的缆机驾驶员操作行为可靠性低,需加强安全培训,严格考核制度,从根本上提高缆机驾驶员操作行为的可靠性,以期提升缆机生产效率,实现预防安全事故的目标.     

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.     

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。     

金属氧化物对十氯联苯的降解研究

分别以市售的Fe2O3、MgO和CaO为催化剂,对十氯联苯(CB209)进行了催化降解研究.结果表明,MgO对CB209的降解具有较高的活性.在反应温度为300℃,反应时间为60 min时,MgO对CB209的降解效率达到98.9%.进一步研究表明,MgO催化降解CB209的动力学符合准一级动力学反应.通过GC-MS和GC-ECD,并结合衍生化实验,检测到九氯联苯、五氯苯和四氯苯、五氯苯酚、四氯苯酚和三氯苯酚等降解产物,进而推测出MgO催化降解CB209的过程中存在相互竞争的反应路径:氧化反应、碳碳桥键断裂和加氢脱氯.     

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.