Retarding and manipulating of DNA molecules translocation through nanopores

Nanopores are emerging sensitive sensors that can detect and analyze single charged molecule. Nanopores present a promising approach for sequencing human gen- ome below US$1,000 because of its superior performance, such as high throughput and low cost. However, a dominant bottleneck, that is, the high translocation speed of DNA molecules, has to be overcome. This property decreases accuracy of nanopore sensors to the single-base level. In this review, we mainly introduce the recent research works of retarding and manipulating of DNA motion through nanopores by actively control of three forces, which are the driving force, interaction force between nanopore and molecule, and exterior drag force. Lastly, conclusion and further outlook are presented pore-based DNA sequencing on future directions of nano- technology.     

Gold nanorod translocation through a solid-state nanopore

Recently, nanopores have been used in an essential technique for detecting single molecule with high sensitivity. The initial application of nanopores to DNA and RNA sequencing has been expanded to sensing pro- teins and nanoparticles, including Bovine serum albumin, silica nanoparticles, polystyrene beads, and others. In our study, for the first time, a positively charged gold nanorod was investigated using a solid-state nanopore device. Various gold nanorods passed through the nanopore with different current blockages and duration times, providing a measurement of the nanorod diameter, length, and charge. Our findings indicate that nanopore sensing might be a new method for characterizing the size, shape, and charge of nanoparticles.     

Detection and analysis of DNA recapture through a solid-state nanopore

Motion control of a single molecule through a solid-state nanopore offers a new perspective on detecting and analyzing single biomolecules. Repeat recapture of a single DNA molecule reveals the dynamics in DNA translocation through a nanopore and may significantly increase the signal-to-noise ratio for DNA base distin- guishing. However, the transient current at the moment of voltage reversal prevents the observation of instantly recaptured molecules and invalidates the continuous DNA ping-pong control. We performed and analyzed the DNA translocation and recapture experiment in a silicon nitride solid-state nanopore. Numerical calculation of molecular motion clearly shows the recapture dynamics with different delay times. The prohibited time when the data acquisition system is saturated by the transient current is derived by equivalent circuit analysis and finite element simulation. The COMSOL simulation reveals that the membrane capacitance plays an important role in determining the electric field distribution during the charging process. As a result of the transient charging process, a non-constant driving force pulls the DNA back to nanopores faster than theoretically predicted. The observed long time constant in the transient current trace is explained by the dielectric absorption of the membrane capacitor.     

Investigation of self-assembled protein dimers through an artificial ion channel for DNA sensing

Artificial nanopores have become promising tools for sensing DNA. Here, we report a new technique for sensing DNA through a conical-shaped nanopore embed- ded in track-etched polyethylene terephthalate （PET） membrane. Two different streptavidin-conjugated mono- valent DNA probes were prepared that can bind to two distinct segments （at either end） of the target DNA. The size of target DNA-linked to the two streptavidin-conju- gated monovalent DNA probes is double that of the indi- vidual probes. By precisely controlling the tip diameter of the conical nanopore embedded in the PET polymer, events due to the translocation of the streptavidin-conjugated monovalent DNA probes through the nanopore can be fil- tered and purposely undetected, whereas the current pulses due to the translocation of the target DNA-induced self- assembled complexes can be detected. The two streptavi- din-conjugated DNA probes cannot be linked by multi- mismatched DNA. Therefore, multi-mismatched （non- specific） DNA will not induce any current pulse signatures. The current pulse signatures for the self-assembled com- plex can be used to confirm the presence of the target DNA. The size-dependent detection of self-assembled complexes on the molecular level shows strong promise for the detection of biomolecules without interference from the probes.     

Towards molecular electronics with large-area molecular junctions

Electronic transport through single molecules has been studied extensively by academic and industrial research groups. Discrete tunnel junctions, or molecular diodes, have been reported using scanning probes, break junctions, metallic crossbars and nanopores. For technological applications, molecular tunnel junctions must be reliable, stable and reproducible. The conductance per molecule, however, typically varies by many orders of magnitude. Self-assembled monolayers (SAMs) may offer a promising route to the fabrication of reliable devices, and charge transport through SAMs of alkanethiols within nanopores is well understood, with non-resonant tunnelling dominating the transport mechanism. Unfortunately, electrical shorts in SAMs are often formed upon vapour deposition of the top electrode, which limits the diameter of the nanopore diodes to about 45 nm. Here we demonstrate a method to manufacture molecular junctions with diameters up to 100 microm with high yields (> 95 per cent). The junctions show excellent stability and reproducibility, and the conductance per unit area is similar to that obtained for benchmark nanopore diodes. Our technique involves processing the molecular junctions in the holes of a lithographically patterned photoresist, and then inserting a conducting polymer interlayer between the SAM and the metal top electrode. This simple approach is potentially low-cost and could pave the way for practical molecular electronics.     

Nanopore-based sensing devices and applications to genome sequencing: a brief history and the missing pieces

A nanopore on an impermeable membrane, which separates two chambers containing electrolytic solu- tion, can be used as a nanometre-sized Coulter counter for single-molecule biological sensing. With an applied poten- tial, charged molecules are electrically dragged through the pore, and the analytical information is sequentially read out from the current blockades. Nucleic acid, which is an elec- trically charged polymer, is an ideal analyte for nanopore analysis and nanopore sequencing. With the advantages of high-speed, label-free and single-molecule resolution, a nanopore sequencer is considered to be the most promising candidate for the third-generation DNA sequencing. In this review, a brief history of nanopore sequencing to date is summarized and discussed along with future prospects. Although successfully demonstrated for known viral gen- ome sequences, the nanopore sequencing technique still requires missing pieces like improved accuracy, automation and throughput for clinical diagnosis-level applications.     

An atomic force microscopy study of coal nanopore structure

Coal nanopore structure is an important factor in understanding the storage and migration of absorbed gas in coal. A new method for studying coal nanopore structures is proposed. This idea is based on the nano-level resolution of atomic force microscopy, which can be employed to observe the structural features of coal nanopores clearly, conduct quantitative three-dimensional measurements and obtain structural parameters. Analysis results show that coal nanopores are mainly metamorphic pores and intermolecul...     

分子动力学模拟烷烃链条数对其在氧修饰石墨烯纳米孔中迁移的影响

为了分析高分子在纳米孔中迁移问题,更好地为纳米器件的设计提供理论支持,采用分子动力学方法模拟了一系列链条数不同的烷烃分子在氧修饰石墨烯纳米孔中的钻孔,研究了链条数N对钻孔条数的影响,给出了均方位移MSD和扩散系数D随N变化的规律.研究结果表明:穿孔条数随着链条数的增加上升明显,但当链条数多到一定程度后,穿孔烷烃数较为缓慢地下降.     

TLM钛合金表面二氧化钛三维结构纳米薄膜的可控制备及表征

为了提高血管支架医用钛合金表面的亲水性和抗溶血作用,采用阳极氧化工艺在近β型TLM(Ti-25Nb-3Mo-2Sn-3Zr)医用钛合金表面构建了具有纳米孔/纳米管三维结构二氧化钛(TiO2)纳米薄膜,并对其结构和性能进行表征.研究结果表明:通过控制一次阳极氧化电压和时间可获得具有上层为无序纳米孔、中层为有序纳米管、底层为有序纳米孔的三维结构TiO2纳米薄膜,该薄膜为无定形态;而采用二次阳极氧化工艺获得了纳米孔互贯网络的TiO2纳米薄膜,该薄膜表面更加平整,且表面孔隙率大、亲水性好,同时具有比一次阳极氧化薄膜更好的抗溶血作用,这为其应用于血管支架方面打下基础.     

四川盆地周缘牛蹄塘组页岩微观孔隙结构特征

以四川盆地周缘地区下寒武统牛蹄塘组富有机质页岩为研究对象,通过X衍射全岩分析、低温液氮吸/脱附等实验方法技术对研究区页岩储层微观孔隙结构进行了系统研究;并探讨了控制纳米尺度微观孔隙结构的主要原因。结果表明:四川盆地周缘牛蹄塘组富有机质页岩矿物组分中石英、长石等脆性矿物含量较高,其次是黏土矿物;页岩微孔结构复杂,多为开放型空隙,以管状孔和平行壁的狭缝状孔为主;微观孔隙孔径主要分布在2~10 nm,以微孔为主。通过分析控制该区页岩储层微观孔隙结构的主要因素,认为有机碳含量是控制纳米级孔隙发育的主要因素,同时也是页岩气赋存的重要物质基础。     

页岩储层纳米孔气体传输耦合模型新研究

页岩气在纳米孔隙的传输过程中受多种因素影响,包括孔隙尺寸和压力、孔隙壁面粗糙度、孔隙力学反应、吸附诱导膨胀反应以及权重因子等。因此需要综合考虑以上因素以及吸附气分子在孔隙中所占空间对气体流动影响的条件下,厘清页岩气的不同运移机制（表面扩散、滑脱流、Knudsen扩散和黏性流动）在不同孔隙尺寸和压力下对纳米孔中总气体流量的贡献率。首先,对页岩气的不同运移方式进行了物理描述及数学表征,然后,在考虑孔隙壁面粗糙度、孔隙力学反应、吸附诱导膨胀反应和权重因子等因素的条件下,建立页岩气在储层纳米孔中的气体传输耦合数学模型,模型可靠性通过格子Boltzmann方法计算结果验证。研究结果表明,当孔径小于10 nm时,纳米孔的总流量主要由表面扩散流量组成,孔径越小,表面扩散流量越大;当孔径为40~250 nm和低压条件下,滑脱流和Knudsen扩散对气体传输影响较大;当孔径大于10 μm时,纳米孔的总流量主要为黏性流量。     

Experimental and molecular dynamics study of gas flow characteristics in nanopores

Gas flow characteristics in nanopores were investigated experimentally and numerically using molecular dynamics (MD) simulations with an emphasis on the friction factor and gas viscosity. The results show that the viscosity and the friction factor in nanopores are much lower than those in macroscale channels. The actual viscosities obtained from the MD studies showed that the gas viscosity in nanopores is less than the macroscale viscosity because collisions between gas molecules are less frequent in high Knudsen number flows and there are more collisions with the wall. The MD simulations show that the velocity profile is composed of two parts, with a much steeper velocity gradient near the wall.     

Ion-beam sculpting at nanometre length scales.

Manipulating matter at the nanometre scale is important for many electronic, chemical and biological advances, but present solid-state fabrication methods do not reproducibly achieve dimensional control at the nanometre scale. Here we report a means of fashioning matter at these dimensions that uses low-energy ion beams and reveals surprising atomic transport phenomena that occur in a variety of materials and geometries. The method is implemented in a feedback-controlled sputtering system that provides fine control over ion beam exposure and sample temperature. We call the method "ion-beam sculpting", and apply it to the problem of fabricating a molecular-scale hole, or nanopore, in a thin insulating solid-state membrane. Such pores can serve to localize molecular-scale electrical junctions and switches and function as masks to create other small-scale structures. Nanopores also function as membrane channels in all living systems, where they serve as extremely sensitive electro-mechanical devices that regulate electric potential, ionic flow, and molecular transport across cellular membranes. We show that ion-beam sculpting can be used to fashion an analogous solid-state device: a robust electronic detector consisting of a single nanopore in a Si3N4 membrane, capable of registering single DNA molecules in aqueous solution.     

带电纳米管道对K离子水合作用影响的模拟研究

采用分子动力学方法模拟了三种不同电荷密度的带电纳米管道对钾离子的水合作用产生的影响.模拟以半径为0.678 nm的无限长单壁椅型带电碳纳米管为纳米管道模型,讨论了在三种不同的电荷密度情况下,钾离子和水分子在管中的径向分布,钾离子水合层中水分子的径向分布以及钾离子第一水合层的水分子数.模拟结果表明,在电荷的影响下,钾离子和水分子在管中的径向分布未有明显的变化,而钾离子水合层的水分子的径向分布以及钾离子第一水合层的水分子数却产生了一定的变化.这说明纳米管道上的电荷会对离子的水合作用产生影响.这些发现将对进一步理解生物离子通道对离子可选择性机理和设计纳米流体器件有一定的意义.     

微生物相互作用研究进展：从观察到预测?

地球上的微生物有着极高的丰富度和多样性.它们的生命活动和相互作用对维持生态系统稳定性起到关键作用;生存在宿主体内的微生物对其宿主的健康有重要影响.第二代测序技术的发展使得科学家获得了大量的关于微生物群落和功能基因组成的数据;而微生物群落和生态系统生态学的重点,正在从获得观测数据转变到理解微生物相互作用过程,并预测群落结构和功能的动态变化.近年来发展了很多针对第二代测序数据的算法和数学模型,以推测微生物种间相互作用网络,但这种自上而下的研究仍存在局限性.自下而上的实验研究可以对微生物种间作用进行直接验证,并帮助我们理解更高层次上的生态学模式和过程.与此同时,基于数学分析或模拟的理论研究展示了微生物相互作用的动态及其对群落动态和功能的影响.今后的研究应该结合观测数据、实验验证、理论模型多种研究方法,增进我们对微生物种间相互作用的理解并做出预测,以应对全球气候变化、传染病暴发、抗生素抗性进化等诸多挑战.     

计算流体力学的微机网络集群系统的研究

介绍了微机集群架构和PVM技术在计算流体力学复杂课题研究中的有效性.着重讨论了在微机并行机群上进行CFD计算,以及计算中的负载平衡等相关问题.给出了并行分区计算的方法,并给出了实际计算结果.结果证明本文介绍的方法是正确的,能有效地均衡计算负载,达到较理想的并行效率.     

多尺度材料计算方法

 在材料基因组科学研究中,多尺度集成材料计算占有不可或缺的地位。本文以微观-介观-宏观材料计算方法中具有代表性的第一原理、分子动力学、计算热力学/动力学及有限元方法为重点,介绍多尺度材料计算方法的基础和应用。     

阳极氧化电压对纳米孔阵列阳极氧化铝膜形貌的影响

阳极氧化铝是将金属铝进行阳极氧化处理后，在其表面上形成的一层氧化膜，可对金属铝起到装饰和保护的作用．20世纪末人们发现，铝在适当的阳极氧化条件下可以制得具有纳米孔阵列的阳极氧化铝膜．随着纳米科学的蓬勃发展，纳米孔阵列阳极氧化铝膜由于其具有大的比表面积、高纵横比、大小均     

Anomalous properties in ferroelectrics induced by atomic ordering.

Complex insulating perovskite alloys are of considerable technological interest because of their large dielectric and piezoelectric responses. Examples of such alloys include (Ba1-xSrx)TiO3, which has emerged as a leading candidate dielectric material for the memory-cell capacitors in dynamic random access memories; and Pb(Zr1-xTix)O3 (PZT), which is widely used in transducers and actuators. The rich variety of structural phases that these alloys can exhibit, and the challenge of relating their anomalous properties to the microscopic structure, make them attractive from a fundamental point of view. Theoretical investigations of modifications to the atomic ordering of these alloys suggest the existence of further unexpected structural properties and hold promise for the development of new functional materials with improved electromechanical properties. Here we report ab initio calculations that show that a certain class of atomic rearrangement should lead simultaneously to large electromechanical responses and to unusual structural phases in a given class of perovskite alloys. Our simulations also reveal the microscopic mechanism responsible for these anomalies.