Determining molecular structures and conformations directly from electron diffraction using a genetic algorithm.

A global optimization strategy, based upon application of a genetic algorithm (GA), is demonstrated as an approach for determining the structures of molecules possessing significant conformational flexibility directly from gas-phase electron diffraction data. In contrast to the common approach to molecular structure determination, based on trial-and-error assessment of structures available from quantum chemical calculations, the GA approach described here does not require expensive quantum mechanical calculations or manual searching of the potential energy surface of the sample molecule, relying instead upon simple comparison between the experimental and calculated diffraction pattern derived from a proposed trial molecular structure. Structures as complex as all-trans retinal and p-coumaric acid, both important chromophores in photosensing processes, may be determined by this approach. In the examples presented here, we find that the GA approach can determine the correct conformation of a flexible molecule described by 11 independent torsion angles. We also demonstrate applications to samples comprising a mixture of two distinct molecular conformations. With these results we conclude that applications of this approach are very promising in elucidating the structures of large molecules directly from electron diffraction data.     

Quantitative High Resolution Electron Microscopy

 With the resolution becoming sufficient to reveal individual atoms, HREM is now entering the stage where it can compete with X-ray methods to quantitatively determine atomic structures of materials without much prior knowledge, but with the advantage of being applicable to aperiodic objects such as crystal defects. In our view the future electron microscope will be characterised by a large versatility in experimental settings under computer control such as the illumination conditions (TEM-STEM), CBED, detecting conditions (diffraction, image, ptychography) and many other tunable parameters such as focus (g), voltage, spherical aberration (C _s ), beam tilt, etc. Since modern detectors can detect single electrons, also the counting statistics is known. The only limiting factor in the experiment will be the total number of electrons that interact with the object during the experiment due to the limitations in the exposure time or in the object damage. However, instrumental potentialities will never be exploited fully if not guided by an experimental strategy. Here intuitive guidelines can be very deceptive. For instance an image made with the best electron microscope (C _s  = 0) at the best focus (g = 0) from the best object (phase object) would show no contrast at all. Hence, questions such as what is the best C _s , focus, object thickness, etc. can only be answered properly if done using a method of experiment design.     

A genetic algorithm for structure-based de novo design

Genetic algorithms have properties which make them attractive in de novo drug design. Like other de novo design programs, genetic algorithms require a method to reduce the enormous search space of possible compounds. Most often this is done using information from known ligands. We have developed the ADAPT program, a genetic algorithm which uses molecular interactions evaluated with docking calculations as a fitness function to reduce the search space. ADAPT does not require information about known ligands. The program takes an initial set of compounds and iteratively builds new compounds based on the fitness scores of the previous set of compounds. We describe the particulars of the ADAPT algorithm and its application to three well-studied target systems. We also show that the strategies of enhanced local sampling and re-introducing diversity to the compound population during the design cycle provide better results than conventional genetic algorithm protocols.     

两种计算吸光光度法同时测定钙镁

研究了在pH10．5的硼砂-氢氧化钾缓冲溶液和乙醇的增敏作用条件下，偶氮氯膦Ⅰ与钙、镁的吸收特性，建立了多波长光度法同时测定钙和镁的方法。采用两种矩阵算法对试验数据进行处理，并对结果进行比较和分析。钙和镁含量在0～25μg／25ml范围内用计算法Ⅱ能得到准确结果。     

On intermediate inquisitive and dependence logics: An algebraic study

This article provides an algebraic study of intermediate inquisitive and dependence logics. While these logics are usually investigated using team semantics, here we introduce an alternative algebraic semantics and we prove it is complete for all intermediate inquisitive and dependence logics. To this end, we define inquisitive and dependence algebras and we investigate their model-theoretic properties. We then focus on finite, core-generated, well-connected inquisitive and dependence algebras: we show they witness the validity of formulas true in inquisitive algebras, and of formulas true in well-connected dependence algebras. Finally, we obtain representation theorems for finite, core-generated, well-connected, inquisitive and dependence algebras and we prove some results connecting team and algebraic semantics.     

Canonical Connections and Algebraic Ricci Solitons of Three-dimensional Lorentzian Lie Groups

In this paper, the author computes canonical connections and KobayashiNomizu connections and their curvature on three-dimensional Lorentzian Lie groups with some product structure. He defines algebraic Ricci solitons associated to canonical connections and Kobayashi-Nomizu connections. He classifies algebraic Ricci solitons associated to canonical connections and Kobayashi-Nomizu connections on three-dimensional Lorentzian Lie groups with some product structure.     

M-矩阵平方根的一类迭代法

矩阵平方根在数学的许多应用中起着重要的作用.本文研究M-矩阵平方根的计算问题,提出一种计算正则M-矩阵平方根的迭代方法.首先将这个问题转化为M-矩阵代数Riccati方程,进而提出一种有效的方法来求解这个特殊的MARE.理论分析表明,该方法在一定条件下是收敛的.数值实验表明该方法是可行的,且优于二项式迭代法.     

Critical exponents,hyperscaling, and universal amplitude ratios for two- and three-dimensional self-avoiding walks

We make a high-precision Monte Carlo study of two- and three-dimensional self-avoiding walks (SAWs) of length up to 80,000 steps, using the pivot algorithm and the Karp-Luby algorithm. We study the critical exponentsv and 2 ₄ – as well as several universal amplitude ratios; in particular, we make an extremely sensitive test of the hyperscaling relationdv = 2 ₄ –. In two dimensions, we confirm the predicted exponentv=3/4 and the hyperscaling relation; we estimate the universal ratios <R _g ² >/<R _e ² >=0.14026±0.00007, <R _m ² >/<R _e ² >=0.43961±0.00034, and ^*=0.66296±0.00043 (68% confidence limits). In three dimensions, we estimatev=0.5877±0.0006 with a correctionto-scaling exponent ₁=0.56±0.03 (subjective 68% confidence limits). This value forv agrees excellently with the field-theoretic renormalization-group prediction, but there is some discrepancy for ₁. Earlier Monte Carlo estimates ofv, which were 0.592, are now seen to be biased by corrections to scaling. We estimate the universal ratios <R _g ² >/<R _e ² >=0.1599±0.0002 and ^*=0.2471±0.0003; since ^*>0, hyperscaling holds. The approach to ^* is from above, contrary to the prediction of the two-parameter renormalization-group theory. We critically reexamine this theory, and explain where the error lies. In an appendix, we prove rigorously (modulo some standard scaling assumptions) the hyperscaling relationdv = 2 ₄ – for two-dimensional SAWs.