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.     

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。     

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.     

相空间重构在语音情感识别中的研究

为了更为全面地表征语音情感状态,弥补线性情感特征参数在刻画不同情感类型上的不足,将相空间重构理论引入语音情感识别中来,通过分析不同情感状态下的混沌特征,提取Kolmogorov熵和关联维作为新的情感特征参数,并结合传统语音特征使用支持向量机（SVM）进行语音情感识别。实验结果表明,通过引入混沌参数,与传统物理特征进行识别的方案相比,准确率有了一定的提高,为语音情感的识别提供了一个新的研究途径。     

一种基于SBL和APIT的混合定位算法

由于子区域分割粒度的限制,基于阶次序列的定位算法(Sequence-based localization,SBL)存在边缘区域节点定位误差较大和不能保证平均定位误差性能的问题。针对这些问题,提出了一种基于SBL和APIT的混合定位算法,利用APIT信标三角形切割SBL算法子区域,减小子区域面积,实现了分割粒度的细化。通过预先进行系统训练,优化了混合算法的加权系数,进一步提升了算法的定位精度。仿真结果表明,相比于原算法,所提出的混合算法有效地提升了边界区域节点的定位精度,其平均定位误差降低了17.9%,使基于阶次序列的定位算法的定位精度得到了有效改善。     

基于排列熵和支持向量机的癫痫发作预测研究

针对癫痫发作给病人带来的巨大伤害,为临床治疗留下足够空余时间,提出一个可以预测癫痫发作的系统模型。对21名癫痫病人进行研究,提取具有较低算法复杂度的排列熵构成特征向量,将其输入支持向量机（support vector machine,SVM）训练出学习模型,用来识别发作期样本,利用投票机制充分考虑病人差异来判断所处状态,最终实现癫痫的实时预测。结果表明,其中81%的发作可以提前平均50多分钟预测到,且具有较低的误报率。为癫痫发作预测系统的理论研究打下坚实基础。     

基于物元分析法的水资源管理现代化评价

为科学合理地评价区域水资源管理现代化水平,从水资源保障、用水效率、水资源保护、水资源公共管理能力、水资源支撑能力5个方面构建评价指标体系,将模糊层次分析法(FAHP)和熵权法耦合,确定评价指标综合权重,基于物元理论建立水资源管理现代化评价模型。以南京市高淳区为例进行评价,结果表明,南京市高淳区水资源现代化管理水平处于初等现代化阶段,与实际情况相符,验证了所构建评价模型的可行性和有效性。     

Efficient multilevel image segmentation through fuzzy entropy maximization and graph cut optimization

The fuzzy c-partition entropy has been widely adopted as a global optimization technique for finding the optimized thresholds for multilevel image segmentation. However, it involves expensive computation as the number of thresholds increases and often yields noisy segmentation results since spatial coherence is not enforced. In this paper, an iterative calculation scheme is presented for reducing redundant computations in entropy evaluation. The efficiency of threshold selection is further improved through utilizing the artificial bee colony algorithm as the optimization technique. Finally, instead of performing thresholding for each pixel independently, the presented algorithm oversegments the input image into small regions and uses the probabilities of fuzzy events to define the costs of different label assignments for each region. The final segmentation results is computed using graph cut, which produces smooth segmentation results. The experimental results demonstrate the presented iterative calculation scheme can greatly reduce the running time and keep it stable as the number of required thresholds increases. Quantitative evaluations over 20 classic images also show that the presented algorithm outperforms existing multilevel segmentation approaches.     

Explicit solution of relative entropy weighted control

We consider the minimization over probability measures of the expected value of a random variable, regularized by relative entropy with respect to a given probability distribution. In the general setting we provide a complete characterization of the situations in which a finite optimal value exists and the situations in which a minimizing probability distribution exists. Specializing to the case where the underlying probability distribution is Wiener measure, we characterize finite relative entropy changes of measure in terms of square integrability of the corresponding change of drift. For the optimal change of measure for the relative entropy weighted optimization, an expression involving the Malliavin derivative of the cost random variable is derived. The theory is illustrated by its application to several examples, including the case where the cost variable is the maximum of a standard Brownian motion over a finite time horizon. For this example we obtain an exact optimal drift, as well as an approximation of the optimal drift through a Monte-Carlo algorithm.     

Entropy of fluidized bed—a measure of particles mixing

The paper presents an attempt to define the physical entropy of the dense phase of a fluidized bed, based on liquid-like properties of fluidized systems. The quantity U was used as the analogy of temperature in classical thermodynamics. The obtained expression for physical entropy was compared to the correlation suggested for the Kolmogorov entropy in bubbling bed.