字符串匹配算法在DNA序列比对中的应用

高通量测序技术的飞速发展让生物信息领域迎来了大数据时代。新技术在提供海量生物遗传信息的同时,也给分析这些数据带来了新的挑战。DNA序列比对是信息分析流程中的关键步骤,为后续的变异检测提供序列比对信息。2015“深圳杯”数学建模夏令营B题以DNA序列比对为研究课题,希望参赛学生给出序列快速比对的最佳方案。本文简要点评了各参赛队伍的解答情况,然后介绍了现有DNA序列比对软件中用到的算法和数据结构。     

Extreme beam attenuation in double-slit experiments: Quantum and subquantum scenarios

Combining high and low probability densities in intensity hybrids  , we study some of their properties in double-slit setups. In particular, we connect to earlier results on beam attenuation techniques in neutron interferometry and study the effects of very small transmission factors, or very low counting rates, respectively, at one of the two slits. We use a “superclassical” modeling procedure which we have previously shown to produce predictions identical with those of standard quantum theory. Although in accordance with the latter, we show that there are previously unexpected new effects in intensity hybrids for transmission factors below a?10⁻⁴$a?10^{-4}$, which can eventually be observed with the aid of weak measurement techniques. We denote these as quantum sweeper effects, which are characterized by the bunching together of low counting rate particles within very narrow spatial domains. We give an explanation of this phenomenology by the circumstance that in reaching down to ever weaker channel intensities, the nonlinear nature of the probability density currents becomes ever more important, a fact which is generally not considered–although implicitly present–in standard quantum mechanics.     

Determination of the Chemical Structure of Poly-β (-)-pinene by NMR Spectroscopy

This paper is dedicated to the memory of our friend and colleague Annalaura Segre.

The chemical structure of a series of β (-)-pinene polymers (PBP) obtained by radiation-induced polymerization, free radical initiation, cationic polymerization over a Friedel-Craft catalyst and by coordinative polymerization over a Ziegler-Natta catalyst has been fully elucidated by ¹H and ¹³C-NMR spectroscopy. 2D NMR techniques have been applied in order to assign all the NMR resonances to the structures of the PBP investigated. The NMR spectra show that the most regular PBP structure is obtained by radiation-induced polymerization followed by the free radical initiated polymerization. The most defective structure has been observed in the case of PBP prepared by cationic mechanism over a Friedel-Crafts catalyst. The discussion accounts for different types of defects and cross-links present in the PBPs investigated whose fundamental structure is based on the p-menthene repeating unit.

NMR self-diffusion measurements have been performed to evaluate the molecular weight of all the PBP investigated. The highest molecular weight (2600 Dalton) was found in the case of PBP prepared by Ziegler-Natta catalyst, while the lowest molecular weight was found in the case of PBP prepared by radiation-induced polymerization (about 1000 Dalton).     

N‐Vinylpyrrolidone and Ethoxyethyl Methacrylate Copolymer: Synthesis,Characterization and Reactivity Ratios

Free radical copolymerization of N‐vinyl‐2‐pyrrolidone with 2‐ethoxyethyl methacrylates was carried out with 2,2′‐azobisisobutyronotrile as an initiator in 1,4‐dioxane. The resulting copolymer was characterized by FTIR, H¹‐NMR and C¹³‐NMR spectroscopic techniques thermal properties of copolymer were determined by DSC and TGA. The reactivity ratios of the monomers were computed by the Fineman‐Rose (F‐R), Kelen‐Tudos (K‐T) and extended Kelen‐Tudos (EK‐T) method at lower conversion, using the data obtained from both FTIR and elemental analysis studies; the results are in good agreement with each other. The average reactivity ratio, Alfrey‐Price Q and e values were found to be r ₁=0.769, r ₂=0.266 and Q ₁=0.0859, e ₁=0.4508, respectively for NVP/EOEMA copolymer. The distribution of monomer sequence along the copolymer chain was calculated using a statistical method based on obtained reactivity ratio. The number average molecular weight and polydispersity were determined by GPC.     

Novel electrochemical biosensor based on functional composite nanofibers for sensitive detection of p53 tumor suppressor gene

A novel electrochemical biosensor based on functional composite nanofibers for sensitive hybridization detection of p53 tumor suppressor using methylene blue (MB) as an electrochemical indicator is developed. The carboxylated multi-walled carbon nanotubes (MWNTs) doped nylon 6 (PA6) composite nanofibers (MWNTs–PA6) was prepared using electrospinning, which served as the nanosized backbone for pyrrole (Py) electropolymerization. The functional composite nanofibers (MWNTs–PA6–PPy) used as supporting scaffolds for ssDNA immobilization can dramatically increase the amount of DNA attachment and the hybridization sensitivity. The biosensor displayed good sensitivity and specificity. The target wild type p53 sequence (wtp53) can be detected as low as 50 fM and the discrimination is up to 57.5% between the wtp53 and the mutant type p53 sequence (mtp53). It holds promise for the early diagnosis of cancer development and monitoring of patient therapy.     

Mild conversion of propargylic alcohols to α,β-unsaturated enones in ionic liquids (ILs); a new ‘metal free’ life for the Rupe rearrangement

A mild and selective transition metal free protocol for the conversion of propargylic alcohols to cyclic and acyclic α,β-unsaturated enones via the Rupe rearrangement is reported. The method utilizes the Brønsted acidic ionic liquid [BMIM-SO₃H][OTf] as catalyst and [BMIM][PF₆] as solvent and offers the potential for recycling and reuse of the IL solvent. The feasibility to synthesize bicyclic fused cyclopentenone derivatives via a Rupe → Aldol → Nazarov sequence utilizing this protocol has also been demonstrated.     

Bridging Ligand Length Controls AT Selectivity and Enantioselectivity of Binuclear Ruthenium Threading Intercalators

The slow dissociation of DNA threading intercalators makes them interesting as model compounds in the search for new DNA targeting drugs, as there appears to be a correlation between slow dissociation and biological activity. Thus, it would be of great value to understand the mechanisms controlling threading intercalation, and for this purpose we have investigated how the length of the bridging ligand of binuclear ruthenium threading intercalators affects their DNA binding properties. We have synthesised a new binuclear ruthenium threading intercalator with slower dissociation kinetics from ct‐DNA than has ever been observed for any ruthenium complex with any type of DNA, a property that we attribute to the increased distance between the ruthenium centres of the new complex. By comparison with previously studied ruthenium complexes, we further conclude that elongation of the bridging ligand reduces the sensitivity of the threading interaction to DNA flexibility, resulting in a decreased AT selectivity for the new complex. We also find that the length of the bridging ligand affects the enantioselectivity with increasing preference for the ΔΔ enantiomer as the bridging ligand becomes longer.     

滴加顺序对制备酯加氢催化剂Cu-Zn-Al-Ba的影响

采用共沉淀法以不同的滴加混合顺序制备了新型高效无铬Cu-Zn-Al-Ba催化剂,通过XRD、SEM、BET、H₂-TPR和TG等表征方式进行了分析,对其前驱体、焙烧后和还原后催化剂物相进行分析研究,探究了相同条件下不同滴加混合顺序对催化剂结构与催化性能的影响,同时考察了催化剂对C12~C18脂肪酸甲酯加氢制醇的催化性能以及重复利用性。结果表明,以混合盐溶液滴加沉淀剂所制备的无铬Cu-Zn-Al-Ba催化剂R-cat具有较好的酯加氢催化活性和稳定性。在230℃,3MPa氢压的反应条件下,R-cat催化C12~C18脂肪酸甲酯加氢制醇的收率和选择性都高于90%,催化剂重复利用5次,仍保持较高的催化活性。     

两大部类持续扩大再生产的优化

基于经典的马克思两大部类社会再生产公式,建立了离散确定型的持续扩大再生产的优化问题的动态规划模型.在生产资料部类的不变资本产出率高于另一部类的条件下,动态规划的指标函数是作为决策变量的生产资料部类积累率的单调函数,因而可以使用逆序解法或者顺序解法,获得唯一的最优策略和最优指标函数.借助《资本论》中的一个举例,计算验证了最优解.