Error analysis of idealized nanopore sequencing

This numerical study provides an error analysis of an idealized nanopore sequencing method in which ionic current measurements are used to sequence intact single‐stranded DNA in the pore, while an enzyme controls DNA motion. Examples of systematic channel errors when more than one nucleotide affects the current amplitude are detailed, which if present will persist regardless of coverage. Absent such errors, random errors associated with tracking through homopolymer regions are shown to necessitate reading known sequences (Escherichia coli K‐12) at least 140 times to achieve 99.99% accuracy (Q40). By exploiting the ability to reread each strand at each pore in an array, arbitrary positioning on an error rate versus throughput tradeoff curve is possible if systematic errors are absent, with throughput governed by the number of pores in the array and the enzyme turnover rate.     

甲硫醇在Cu(111)表面的解离吸附: 密度泛函理论研究

采用基于密度泛函理论的第一性原理方法和平板模型研究了CH₃SH分子在Cu(111)表面的吸附反应.系统地计算了S原子在不同位置以不同方式吸附的一系列构型, 第一次得到未解离的CH₃SH分子在Cu(111)表面顶位上的稳定吸附构型,该构型吸附属于弱的化学吸附, 吸附能为0.39 eV. 计算同时发现在热力学上解离结构比未解离结构更加稳定. 解离的CH₃S吸附在桥位和中空位之间, 吸附能为0.75-0.77 eV. 计算分析了未解离吸附到解离吸附的两条反应路径, 最小能量路径的能垒为0.57 eV. 计算结果还表明S―H键断裂后的H原子并不是以H₂分子的形式从表面解吸附而是以与表面成键的形式存在. 通过比较S原子在独立的CH₃SH分子和吸附状态下的局域态密度, 发现S―H键断裂后S原子和表面的键合强于未断裂时S原子和表面的键合.     

水在HfO2(111)和(110)表面的吸附与解离

运用广义梯度近似密度泛函理论方法(GGA-PW91)结合周期平板模型, 研究水分子在二氧化铪(111)和(110)表面不同吸附位置在不同覆盖度下的吸附行为. 通过比较不同吸附位的吸附能和几何构型参数发现:(111)和(110)表面铪原子(top 位)是活性吸附位. 水分子与表面的吸附能值随覆盖度的变化影响较小. 在(111)和(110)表面, 水分子都倾向以氧端与表面铪原子相互作用. 同时也计算了羟基、氧和氢在表面的吸附, Mulliken 电荷布居, 态密度及部分频率. 结果表明, 在两种表面羟基以氧端与表面铪相互作用, 氧原子与表面铪和氧原子同时成键, 而氢原子直接与表面氧原子相互作用形成羟基. 通过过渡态搜索, 水分子在(111)和(110)表面发生解离, 反应能垒分别为9.7和17.3 kJ·mol^-1, 且放热为59.9和47.6 kJ·mol^-1.     

水分子对α相CL-20热分解机理影响的分子动力学研究

研究六硝基六氮杂异伍兹烷(CL-20)晶体不同晶型在不同温度下的反应机理, 对于深入认识含能材料在极端条件下的冲击起爆、冲击点火和爆轰过程等具有重要意义. 基于反应力场, 研究水分子在纯α相CL-20及其水合物的晶体结构中数量随时间的变换, 分析水分子对两种体系的初始分解和第二阶段的分解路径的影响. 计算结果表明: CL-20 分子的初始分解路径与水分子无关, 第二阶段的分解反应与水分子有关. 在低温(T<1500 K)下, 水分子对两种体系没有影响, 二者的初始分解路径均为N-NO₂键生成NO₂自由基; 在1500 K≤T≤2500 K时, 水分子作为反应物或与NO₂、、OH自由基等组成催化体系, 生成O₂、H₂O₂等产物, 加速水合物体系在高温下的第二阶段反应, 使得高温下水合物体系的化学反应速率和反应生成的NO₂自由基的数量比纯CL-20体系的化学反应速率和反应生成的NO₂自由基的数量大; 在T>2500 K时, 水分子的催化反应抑制CL-20初始分解反应, 使得在3000 K时纯CL-20体系的反应速率大于水合物体系中CL-20的反应速率.     

超薄油膜润滑的分子动力学模拟Ⅰ．刚性分子模型

分子量级超薄油膜的润滑特性与流体润滑及边界润滑的都有所不同，而且在超薄油膜中也同样存在着润滑剂的流动。因此，利用分子动力学方法模拟了超薄油膜中的压力流动，模拟中采用了刚性分子流体模型，重点研究固体壁面对流动的影响，结果表明，当油膜厚度远比流体分子“直径”大时，模拟所得速度剖面和流量均与流体力学的理论值基本一致；随着油膜厚度逐渐变薄，压力流动或动压流因受到固体壁面的阻碍作用而不断减小；当油膜厚度减小到几个分子直径量级时，两固体壁面之间的流体分子发生固化或晶体化，由此而导致压力流动消失。这可能是流体动力润滑向边界润滑转化的机理之一。由这些研究结果可见，分子动力学模拟在薄膜润滑研究中具有广阔的应用前景。     

长程铯里德堡分子的势能曲线

本文介绍了半经典近似下的低能电子-原子散射理论, 引入贋势描述里德堡电子与基态原子的相互作用, 数值计算了铯原子nS (n=30-60)里德堡态与6S基态原子形成的长程里德堡分子的势能曲线. 并对最外层势阱进行分析, 获得长程里德堡分子的势阱深度、平衡距离与主量子数n的关系. 为实验制备里德堡分子并进一步分析其性质提供理论依据. 里德堡分子对外界非常敏感, 可用于微弱信号的检测.     

飞秒脉冲激光啁啾对4,4’-二(二正丁胺基)二苯乙烯的光限幅及动态双光子吸收的影响(英文)

通过采用预估矫正的时域有限差分方法(FDTD)数值求解Maxwell-Bloch方程,研究飞秒啁啾脉冲激光在4,4’-二(二正丁胺基)二苯乙烯(BDBAS)分子介质中的光限幅行为(OL)和动态双光子吸收(TPA)截面.计算表明啁啾率的符号和大小都对频谱演化和光限幅行为产生影响.啁啾率的符号决定频移的方向:正啁啾对应频谱蓝移,负啁啾对应频谱红移.随着啁啾率绝对值的增大,频移更加明显,光限幅窗口变窄,同时出射光强饱和值变大.有趣的是,当负啁啾降低到一定值(-0.025/fs2)时,出现自感应透明(SIT)现象.另外,动态双光子吸收截面在考虑啁啾效应的情况下减小.本研究提供了一种控制非线性光学吸收的方法.     

Influence of one CO molecule on structural and electronic properties of monatomic Cu chain

By using first-principles calculations, we have systematically investigated the structural and electronic properties of an infinite linear monatomic Cu chain with an adsorbed CO molecule. We find that the bridge geometry is energeticabsally favored not only when the Cu–Cu bond below the molecule is unstretched, but also for a wide range of d_Cu–Cu up to about 4.20 Å, while the substitutional geometry is favored only in the hyperstretched situation d_Cu–Cu>4.80 Å. Charge density differences point out the electron transfer is from the Cu atoms to the adsorbed CO molecule. The binding mechanism of CO to Cu chain can be described by the Blyholder’s model, in terms of σ-donation of electron density from the nonbonding CO-5σ orbital into empty metal orbitals and π-backdonation from the occupied metal d orbitals to empty CO-2π^⁎ orbital. The donation/backdonation process leads to the formation of bonding/antibonding pairs, 5σ_b/5σ_a and 2π_b^⁎/2π_a^⁎, with the 5σ_a lying above E_f and the 2π_b^⁎ below E_f.     

Immunosensor for Detection of the Textile Dye Disperse Orange 1 Based on Non‐conventional Competitive Assay

Textile dyes appear as an important class of compounds that has become a matter of public concern and a serious challenge for scientists and environmentalists due to their large‐scale production and extensive application. In this work, a non‐conventional competitive‐type amperometric immunosensor was successfully developed for detection of the textile dye Disperse Orange 1 (DO1). The DO1 was magnetically captured and separated from the sample solution using magnetic particles (MP) functionalized with the antibody anti‐DO1 and with HRP and gold electrodes were modified with the conjugate DO1‐BSA. Molecules of DO1 immobilized on the electrode surface and DO1 captured by MP compete for antibody binding sites. As a result, the amperometric signal decreases with increasing target DO1 concentration at the capture step, because this decreases, the attachment between the HRP coated MP and the electrode. This strategy allowed us to determine DO1 at the low detection limit of 0.87 ng mL^?1 with great specificity. Also, there were good recoveries for detection of the textile dye in river water samples without the need of sample pre‐treatment. The competitive amperometric immunosensor shows applicability for the determination of small molecules that cannot be determined by conventional competitive or sandwich immunosensors.     

Single‐Molecule Study of a Plasmon‐Induced Reaction for a Strongly Chemisorbed Molecule

Chemical reactions induced by plasmons achieve effective solar‐to‐chemical energy conversion. However, the mechanism of these reactions, which generate a strong electric field, hot carriers, and heat through the excitation and decay processes, is still controversial. In addition, it is not fully understood which factor governs the mechanism. To obtain mechanistic knowledge, we investigated the plasmon‐induced dissociation of a single‐molecule strongly chemisorbed on a metal surface, two O₂ species chemisorbed on Ag(110) with different orientations and electronic structures, using a scanning tunneling microscope (STM) combined with light irradiation at 5 K. A combination of quantitative analysis by the STM and density functional theory calculations revealed that the hot carriers are transferred to the antibonding (π*) orbitals of O₂ strongly hybridized with the metal states and that the dominant pathway and reaction yield are determined by the electronic structures formed by the molecule–metal chemical interaction.