Accurate Receptor-Ligand Binding Free Energies from Fast QM Conformational Chemical Space Sampling

Small molecule receptor-binding is dominated by weak, non-covalent interactions such as van-der-Waals hydrogen bonding or electrostatics. Calculating these non-covalent ligand-receptor interactions is a challenge to computational means in terms of accuracy and efficacy since the ligand may bind in a number of thermally accessible conformations. The conformational rotamer ensemble sampling tool (CREST) uses an iterative scheme to efficiently sample the conformational space and calculates energies using the semi-empirical ‘Geometry, Frequency, Noncovalent, eXtended Tight Binding’ (GFN2-xTB) method. This combined approach is applied to blind predictions of the modes and free energies of binding for a set of 10 drug molecule ligands to the cucurbit[n]urils CB[8] receptor from the recent ‘Statistical Assessment of the Modeling of Proteins and Ligands’ (SAMPL) challenge including morphine, hydromorphine, cocaine, fentanyl, and ketamine. For each system, the conformational space was sufficiently sampled for the free ligand and the ligand-receptor complexes using the quantum chemical Hamiltonian. A multitude of structures makes up the final conformer-rotamer ensemble, for which then free energies of binding are calculated. For those large and complex molecules, the results are in good agreement with experimental values with a mean error of 3 kcal/mol. The GFN2-xTB energies of binding are validated by advanced density functional theory calculations and found to be in good agreement. The efficacy of the automated QM sampling workflow allows the extension towards other complex molecular interaction scenarios.     

基于相对熵的KNN文本分类方法的研究

摘要:为提高处理文本相似度的效果,提出了一种基于相对熵度量文本差异的KNN算法.该算法首先对文本进行预处理(分字与删去停用字)和构建特征字字典; 然后计算训练集中所有文本特征字的概率,并组成训练集(特征字概率矩阵); 最后计算预测文本的特征字概率向量,并通过计算和统计K个预测文本与训练集文本间相对熵最小的文本类别个数后将数目最多的类别作为测试样本的类别.实验结果表明,该算法的分类效果不仅显著优于传统KNN、SVM、Decision Tree、朴素Bayes算法的分类效果,且在小样本数据情况下     

传热推动力损耗的温度场熵分析

运用物理场熵的概念,以传热推动力在空间温度场中不可逆损耗,定量表达传热过程不可逆程度,并将温度场熵分析法应用于矩形散热翅片效率的研究,得到温度场熵与翅片长度成正比、与厚度和导热系数成反比的定量关系。并通过与翅片散热效率曲线对比表明,温度场熵不仅反映了传热过程中系统的热力性能和热效,而且揭示了翅片热效变化的内在机理,对优化此类热力系统的设计具有实际应用价值。     

化工过程熵增指数及其在磷复肥清洁生产评价中的应用

从热力学第二定律出发, 指出清洁生产的热力学本质是控制物质由有序结构向无序转化并从中获取最大效益, 其优劣可由过程熵增反映。 引用复杂体系非平衡定态过程最小熵产生原理,推导出依据与外界交换的物流和热流信息定量计算化工复杂系统过程熵增的方法, 并定义过程熵增指数ζ 。 评价了化工过程对环境热力学状态的综合影响。选择以硫和以氨为载能原料的磷复肥工艺为例进行了计算和对比,其过程熵增指数分别为6.753和4.571,反映出载能原料硫作为废物排放对环境热力学状态产生更大的影响。     

江苏省磷资源安全评价与演化趋势

通过系统的资料整理与严密的数据分析,在阐述省内磷资源概况与化肥施用需求的基础上,依据熵值法修正的层次分析法建立了农用矿产资源的安全评价体系。修正的安全系数和最终计算结果更加符合实际,显示了该方法的科学性、优越性。评价结果表明:江苏省磷资源安全演化整体呈下降趋势,结合省内情况可分为4个阶段。资源禀赋是影响农用矿产安全的主要因素,其次是化肥施用量、勘查资金投入等因素,据此强调开拓市场、科学施肥、保护环境。模型的建立及结果对资源产业持续健康发展和区域经济社会发展具有参考意义。     

An understanding of high entropy alloys from phase diagram calculations

The concept of High Entropy Alloy (HEA) is understood from the point of view of phase diagram calculation. The role of entropy of mixing on the phase stability is discussed for both ideal and non-ideal solid solution phases. The relative stability of a solid solution phase and line compounds is illustrated using hypothetical systems. Calculated binary and multicomponent phase diagrams are used to explain the phenomena observed experimentally for HEAs. The potential of using the CALPHAD (CALculation of PHAse Diagrams) approach in aiding the design of alloys with multiple key components is also discussed.     

淮河流域水资源短缺风险评估与时空分析

根据2003-2013年淮河流域五省的降水量、径流系数、人均水资源量、人均GDP、人口密度等相关数据,构建水资源短缺风险评价体系,用熵权法对指标赋值,运用可变模糊模型对淮河流域及各省的水资源短缺风险进行评估和时空差异分析。结果表明:2003-2013年间淮河流域水资源短缺风险值总体较高,且呈缓慢的增长趋势,2004年降水较少,风险值达到最高;十年间河南省风险增加最为明显,而山东省较为稳定,风险增加也最低;在淮河流域五个区域中,河南省的风险程度最高,达到3.52;江苏省、山东省次之;安徽省和湖北省相对较低,达到2.86和2.51。水资源短缺风险二级指标分析发现,危险性最强的是河南省,安徽省最小;水资源短缺易损性最强的是山东省,湖北省最小;水资源短缺暴露性最强的是江苏省,山东省最小;水资源短缺可恢复性最好的是湖北省,河南省最差。同时,所有评价指标中人口密度、人均GDP、降水量对水资源短缺风险的影响较大。     

基于DPSIR和主成分分析的阜康市水资源承载力评价

针对新疆自治区阜康市水资源日益短缺及生态环境逐渐恶化的现实情况,根据DPSIR框架展开水资源承载力因子分析,构建了水资源承载力多因素基础指标体系;应用主成分分析法筛选出主要指标,采用熵权法进行赋权;构建综合评价模型对水资源承载力进行计算。研究表明:筛选出的4个主成分累计贡献率为92.016%,能充分代表多因素基础指标体系;阜康市九年间(2006年-2014年)水资源承载力综合评分值在0.498~0.531之间波动,下降速率缓慢且波动幅度减小,整体上处于开发饱和阶段。社会和经济发展的压力带来的农业用水的增加是导致水资源承载力下降的主要指标,扩大地下水开采和推行的节水灌溉等压采措施则在很大程度上缓解了下降的趋势。     

Personalized identification of abdominal wall hernia meshes on computed tomography

An abdominal wall hernia is a protrusion of the intestine through an opening or area of weakness in the abdominal wall. Correct pre-operative identification of abdominal wall hernia meshes could help surgeons adjust the surgical plan to meet the expected difficulty and morbidity of operating through or removing the previous mesh. First, we present herein for the first time the application of image analysis for automated identification of hernia meshes. Second, we discuss the novel development of a new entropy-based image texture feature using geostatistics and indicator kriging. Third, we seek to enhance the hernia mesh identification by combining the new texture feature with the gray-level co-occurrence matrix feature of the image. The two features can characterize complementary information of anatomic details of the abdominal hernia wall and its mesh on computed tomography. Experimental results have demonstrated the effectiveness of the proposed study. The new computational tool has potential for personalized mesh identification which can assist surgeons in the diagnosis and repair of complex abdominal wall hernias.     

无约束非线性lp问题的区间极大熵方法

针对信号处理、系统识别等领域中涉及到的无约束非线性lp问题,为减小由于二进制编码的舍入误差对该问题计算结果的影响,对求解该问题的极大熵方法进行了区间扩张.证明了区间扩张后的极大熵函数至少具有二阶收敛性,并设计了具有多项式时间复杂度的区间算法进行求解,举例进行了数值计算.数值计算结果显示,该区间算法可靠,计算结果与区间扩张前相比,结果更加精确.