Translocation of DNA oligonucleotide through carbon nanotube channels under induced pressure difference

This paper presents molecular dynamics (MD) simulations of DNA oligonucleotide and water molecules translocating through carbon nanotube (CNT) channels. Induced pressure difference is applied to the system by pushing a layer of water molecules towards the flow direction to drive the oligonucleotide and other molecules. This novel MD simulation investigates the flow behaviour of oligonucleotide and water molecules in nanochannel while controlling the temperature and volume of the system in canonical ensemble. The results show that the oligonucleotide is unable to translocate through the (8, 8)-(12, 12) CNT channel under the induced pressures applied. However, the oligonucleotide can transport through the (10, 10)-(14, 14) CNT channel easily under the same induced pressures. It is observed that less water molecules permeate through the center of the (8, 8)-(12, 12) CNT channel as the strength of the induced pressure is increased. In contrast, more water molecules flow through the (10, 10)-(14, 14) CNT channel at a higher induced pressure. The conformational energy of the oligonucleotide in the CNT channels has been shown to be affected by both the strength of the induced pressure and the size of the nanotube. Although the interactive force between oligonucleotide and CNT channel is dependent on their distance apart, the induced pressure within the (8, 8)-(12, 12) nanotube channel acts as an external factor that affects the distance between the oligonucleotide and the CNT junction. The insertion depth of the oligonucleotide in the (8, 8)-(12, 12) CNT channel relies on the magnitude of the induced pressure. Both the velocity of oligonucleotide and the interactive force between oligonucleotide and nanotube wall are shown to increase when the oligonucleotide is travelling through the narrower part of the (10, 10)-(14, 14) CNT channel.     

Impact of thermostat on interfacial thermal conductance prediction from non-equilibrium molecular dynamics simulations

The knowledge of interfacial thermal conductance (ITC) is key to understand thermal transport in nanostructures. The non-equilibrium molecular dynamics (NEMD) simulation is a useful tool to calculate the ITC. In this study, we investigate the impact of thermostat on the prediction of the ITC. The Langevin thermostat is found to result in larger ITC than the Nose-Hoover thermostat. In addition, the results from NEMD simulations with the Nose-Hoover thermostat exhibit strong size effect of thermal reservoirs. Detailed spectral heat flux decomposition and modal temperature calculation reveal that the acoustic phonons in hot and cold thermal reservoirs are of smaller temperature difference than optical phonons when using the Nose-Hoover thermostat, while phonons in the Langevin thermostat are of identical temperatures. Such a non-equilibrium state of phonons in the case of the Nose-Hoover thermostat reduces the heat flux of low-to-middle-frequency phonons. We also discuss how enlarging the reservoirs or adding an epitaxial rough wall to the reservoirs affects the predicted ITC, and find that these attempts could help to thermalize the phonons, but still underestimate the heat flux from low-frequency phonons.     

Pressure-induced hemolysis of in vivo aged human erythrocytes is enhanced by inhibition of water transport via aquaporin-1

Human erythrocytes are fractionated into young, intermediate, and old cells according to their densities. Pressure-induced hemolysis reflects sensitively membrane perturbations. Therefore, the hemolysis of erythrocytes at 200 MPa was examined using fractionated cells. Pressure-induced hemolysis of old (or in vivo aged) erythrocytes was enhanced, compared with those of young and intermediate cells which showed the same hemolytic values. Flow cytometric analysis showed less fragmentation of old erythrocytes under pressure. Moreover, the water transport through the membrane was suppressed in old erythrocytes than intermediate ones. The low permeability of water in old erythrocytes was confirmed by osmotic hemolysis using a hypotonic buffer. These results suggest that water transport via aquaporin-1 (AQP1) is inhibited in old erythrocytes. As the number of AQP1 molecules remained constant in old erythrocytes, the function of AQP1 may be reduced.     

A simulation study of the pore size dependence of transport selectivity in cylindrical pores

The equilibrium adsorption and transport properties of mixtures of methane and carbon dioxide, modelled as spherical molecules, have been studied in cylindrical model pores with graphitic properties over a range of cylinder radii. The equilibrium isotherms exhibit packing transitions similar to those observed for single adsorbates; as a consequence, optimum separation factors are found at particular radii, depending on the fugacity (or pressure) in the system. The equations of non-equilibrium thermodynamics have been developed so as to represent the flux of each component in a Fickian form, as a coefficient multiplying the gradient of the total density. Diffusion coefficients were calculated from streaming velocity correlations and NEMD was used to obtain the ‘apparent’ viscous component. The results show that diffusion coefficients from equilibrium molecular dynamics and viscous diffusion coefficients from non-equilibrium calculations are identical within the errors of the calculation. It follows that equilibrium and dynamic separation factors have the same values over a range of pore sizes.     

Solvothermal synthesis of high hydrogen permeable Pd/Ag alloy particles and their hydrogen transport properties

Pd₇₆Ag₂₄ nanoparticles with high purity and a face-centered cubic structure were prepared using a solvothermal method. The lattice parameter of the Pd₇₇Ag₂₃ nanopowders (space group 225Fm3m) was calculated to be a?=?3.9382 Å. The primary particle size was calculated to be 7.7 nm from the X-ray line width using the Scherrer formula, and the interplanar distances was estimated to be 2.272 and 2.000 Å based on indexing on the (111) and (200) plane, respectively. These values are slightly larger than those of pure Pd and smaller than Ag in the (111) plane. The linear relationship of the hydrogen permeation flux with the square root of the hydrogen partial pressure gradient across a 0.26-mm-thick Pd/Ag-YSZ cermet membrane confirmed the major hydrogen transport through the Pd/Ag phase of cermet membranes. The Pd/Ag-YSZ cermet membranes showed significantly higher hydrogen permeation flux than the Pd-YSZ cermet membrane, even though the activation energy for the Pd/Ag alloy cermet membranes showed slightly higher values than that of the Pd cermet membranes. The hydrogen–oxygen dual flux through Pd/Ag-YSZ cermet membranes was confirmed by the maximum hydrogen production by combining the ability of hydrogen production from water with the function of hydrogen separation on composite membranes     

Flux in the Case of Gaussian White Noises

The transport of a spatially periodic system driven by additive and multiplicative Gaussian white noises (between which there is a correlation function) is investigated. The probability current (flux) shows .that the correlation function between the additive and multiplicative noises, and the spatial asymmetry are ingredients for the flux of particles. It is a new phenomenon that the correlation function between the additive and multiplicative noises can cause transport.     

Water Transport through Multinanopores Membranes

We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule distribution in nanopore and average water flow are obtained. It is found that the average water molecule number and water flow are slightly different between a system made of the neighbouring nanopores and a system of a single pore. This indicates that transport of water chains in neighbouring pores do no show significant influence each other. These findings should be helpful in designing efficient artificial membrane made of nanopores and providing an insight into effects of the biological channel structure on the water permeation.     

Hydrogen permeation of tungsten phosphate glass thin films

Thin films of tungsten phosphate glasses were deposited on a Pd substrate by a pulsed laser deposition method and the flux of hydrogen passed thorough the glass film was measured with a conventional gas permeation technique in the temperature range 300–500 °C. The glass film deposited at low oxygen pressure was inappropriate for hydrogen permeation because of reduction of W ions due to oxygen deficiency. The membrane used in the hydrogen permeation experiment was a 3-layered membrane and consisted of Pd film (~ 20 nm), the glass film (≤ 300 nm) and the Pd substrate (250 µm). When the pressure difference of hydrogen and thickness of the glass layer were respectively 0.2 MPa and ~ 100 nm, the permeation rate through the membrane was 2.0 × 10^? 6 mol cm^? 2 s^? 1 at 500 °C. It was confirmed that the protonic and electronic mixed conducting glass thin film show high hydrogen permeation rate.     

在高压诱导蛋白质变性过程中水产生的压缩对它的影响

实验表明水的压缩系数随着压强的改变会发生变化,这种改变将对高压致蛋白质变性的充分含水动力学模拟结果产生直接影响,然而很多高压变性的分子动力学模拟并没有考虑这一点.在温度为300 K,压强为200 MPa、1000 MPa时,利用GROMACS软件包对两种小蛋白Chignolin和Trpcage进行了总计300ns的分子动力学模拟,模拟中考虑了水的压缩系数随压强的改变情况,然后将模拟结果与压缩系数维持在O.1 MPa时的情况进行了比较.结果发现,压缩系数对蛋白质高压变性的影响很大,依据实验数据对不同压强的压缩系数进行调整后,小蛋白Chignolin在高压变性中出现完全去折叠.这为分子动力学模拟研究蛋白质高压变性提供了正确的途径和理论依据.     

Nonequilibrium molecular dynamics simulation of shear viscosity by a uniform momentum source-and-sink scheme

A uniform momentum source-and-sink scheme of nonequilibrium molecular dynamics (NEMD) is developed to calculate the shear viscosity of fluids in this paper. The uniform momentum source and sink are realized by momentum exchanges of individual atoms in the left and right half systems, like the reverse nonequilibrium molecular dynamics (RNEMD) method [20] [Müller-Plathe, Phys. Rev. E, 49 (359), 1999]. This method has all features of RNEMD. In addition, the present momentum swap strategy maximizes the perturbation relaxation and eliminates the boundary jumps, which often harm other NEMD methods greatly. With periodic boundary conditions quadratic velocity profiles can be constructed and from the mean velocities of the right and left half systems the shear viscosity can be easily extracted. The scheme is tested on Lennard-Jones fluids over a wide range of state points (temperature and density), momentum exchange intervals and system sizes. It is demonstrated that the present approach can give reliable results with fast convergence by properly selecting the simulation parameters, i.e. particle number and exchange interval.     

碳纳米管-石墨烯纳米带过渡连接处的力学稳定性与热传导性质研究

任何的非平面连接,材料连接处的材料失配都能导致材料局部或整体性质的改变.本文以纵向拉开的碳纳米管(CNT)为研究对象,采用非平衡态分子动力学(NEMD)的模拟方法,通过改变CNT纵向拉开的剧烈程度,即CNT向石墨烯纳米带(GNR)过渡转变的开角大小,研究其力学稳定性和热传导性质的变化.结果表明,CNT到GNR的过渡越剧烈,连接处的开角越大,其局部热导率越高,单位长度的热阻越小;对于不同管径的CNT来说,连接处的最大开角恒定不变,为16.3°.     

单晶硅薄膜法向热导率分子动力学研究

采用非平衡分子动力学方法（NEMD）研究了平均温度为 500K、厚度为 2～32nm的单晶硅薄膜的法向热导率。模拟结果表明,薄膜热导率显著低于对应温度下的体硅单晶的实验值,并随膜厚度减小以接近线性的规律减小。用声子气动力论模型的分析结果与NEMD模拟相一致,表明纳米单晶硅薄膜中声子平均自由程显著减小。     

Nanoscale thermal cloaking by in-situ annealing silicon membrane

With the advent of thermal metamaterials, many new thermal functionalities have been proposed, like thermal cloaking, concentrating, etc. However, these thermal functionalities are based on the transformation thermotics or scattering cancellation technique, which, derived from Fourier's law, cannot apply to the micro-/nanoscale counterparts. In this paper, we design a nanoscale thermal cloak based on a crystalline silicon (Si) membrane and investigate the in-plane phonon transport via non-equilibrium molecular dynamics (NEMD) simulation by in-situ tuning the thermal conductivity of the thermal cloak from crystalline Si to amorphous Si. The two-dimensional temperature profile is obtained, and the thermal cloaking effect is evaluated by the ratio of heat flux. By analyzing the phonon density of state (PDOS) and the mode participation ratio (MPR), the mechanism can be attributed to the phonon localization in the annealed cloaking region. The proposed nanoscale thermal cloak by in-situ tuned thermal conductivity, may trigger the development of nanoscale thermal functionalities and open avenues for and thermal management for nano-photonics and nano-electronics.     

低维限域结构中水与物质的输运

低维限域结构中水与物质的输运研究,对于解决界面化学和流体力学中的遗留问题十分关键.近年来,研究人员采用分子动力学模拟和实验手段研究低维限域结构中水与物质的输运,并将其应用于物质输运、纳米限域化学反应、纳米材料制备等领域.本文从理论和实验的角度总结一维和二维纳米通道的水与物质输运,介绍了本研究组提出的"量子限域超流体"概念,并用于解释纳米通道中超快物质的输运现象;在此基础上概述了一维纳米通道中的分子动力学模拟和水浸润性,以及外部环境(如温度和电压)对限域结构中水浸润性的调控,同时阐述了低维限域结构中的液体输运;对二维纳米通道中的分子动力学模拟、液体浸润性以及液体输运进行了综述;讨论了纳米通道限域结构在物质输运、纳米限域化学反应和纳米材料制备等领域的应用;对低维限域结构中水与物质输运面临的挑战和前景进行了展望.     

Oxygen permeability of CaTi0.8Fe0.2O3-δ

The oxygen permeation through a dense ceramic membrane with the composition CaTi_0.8Fe_0.2O_3-δ has been measured as a function of the oxygen partial pressure gradient across the membrane at high temperatures (1000, 1050 °C). The permeation current dependence on the oxygen pressure gradient indicates that bulk diffusion controls the oxygen transport rate in the membrane under moderate oxygen pressure gradients, while the surface exchange limits the oxygen permeation at high oxygen pressure gradients. An oxygen concentration drop appears at the membrane-gas boundary.     

水蒸气对二氧化硅膜的影响：吸附性能与渗流效应

研究了在50和90 oC时水蒸气对孔径约为4 ?的二氧化硅膜的吸附性能和渗流效应影响,采用椭圆偏振光谱分析水蒸气的吸附性能,以及测定氦气-H₂O二元混合气体的透过性能. 研究表明水蒸气在二氧化硅膜上的吸附行为符合一阶Langmuir等温线,同时,在H₂O分子存在的条件下,氦气的透过率会急剧下降. 通常,在极小孔内气体分子的传输被认为是不连续的,而是在势能下从一个占有位置跳跃到另外一个空位上. 当在二氧化硅表面的H₂O分子覆盖率上升时,氦气的透过率急剧下降可能与渗流效应有关,其中吸附在二氧化硅表面的H₂O分子阻碍了氦气分子的跳跃.     

石墨烯碳纳米管复合结构渗透特性的分子动力学研究

采用经典分子动力学方法研究了压力驱动作用下水在石墨烯碳纳米管复合结构中的渗透特性.研究结果表明,水分子渗透通过石墨烯碳纳米管复合结构的渗透率明显高于石墨烯碳纳米管组合结构.水在石墨烯碳纳米管复合结构中的渗透率随着压强的升高而增大,随着电场强度的增大而减小.考虑了温度和复合结构中双碳管轴心距对水渗透性的影响规律.系统温度越高,水的渗透率越高;随着双碳管轴心距的增加,水的渗透率逐渐降低.通过计算分析水流沿渗透方向的能障分布,解释了各参数变化对水在石墨烯碳管复合结构中渗透特性的影响机理.研究结果将为基于石墨烯碳管复合结构的新型纳米水泵设计提供一定的理论依据.     

一种模拟热导率的非平衡分子动力学方法

提出一种计算热导率的非平衡分子动力学(NEMD)方法,通过构造均匀内热源获得抛物线形温度分布,并基于Fourier导热定律计算热导率,与Müller-Plathe发展的反扰动非平衡分子动力学(RNEMD)方法相比,不仅具有能量动量守恒和收敛性好的优点,还克服了常规NEMD方法中热冷源区域存在局域热力学非平衡的问题,并有模拟系统温差影响小的特点.对液态氩的热导率进行模拟并与RNEMD方法的模拟结果进行对比.     

A transient TGA study on oxygen permeation properties of perovskite-type ceramic membrane

This paper reports transient weight curves of La_0.2Sr_0.8CoO_3−δ (LSC) membrane (crashed in small grains) subject to an instantaneous change of oxygen activity in the gas phase. When the surrounding gas changes between pure oxygen and helium, the LSC sample experiences a slow weight loss in the oxygen desorption period and a rapid weight gain in the oxygen absorption period due mainly to the difference in the driving force. The LSC sample undergoes phase transformation/chemical reaction with the surrounding gas changing between the pure oxygen and methane. A mathematical model considering surface reaction as the rate-limiting step is presented to describe the oxygen transport through the membrane material, and employed to obtain the surface reaction rate constants. A simple correlation between the oxygen permeation flux and rate constants measured by the transient thermogravimetric analysis (TGA) method is given. The oxygen permeation fluxes calculated from the data measured by the present TGA method are consistent with the data measured by the permeation method. The TGA method is found particularly useful for studying the surface reaction rates of oxygen permeation through thin mixed-conducting ceramic membranes.     

Preparation of poly(vinyl alcohol)–silicone based hybrid membranes for the pervaporation separation of water–acetic acid mixtures

Hybrid membranes were prepared using poly(vinyl alcohol) (PVA) and tetraethylorthosilicate (TEOS) via hydrolysis followed by condensation. The obtained membranes were characterized by Fourier transform infrared spectroscopy, wide-angle x-ray diffraction and differential scanning calorimetry. A remarkable decrease in degree of swelling was observed with increasing TEOS content in membranes and is attributed to the formation of hydrogen bonding and covalent bonds in the membrane matrix. The pervaporation performance of these membranes for the separation of water–acetic acid mixtures was investigated in terms of feed concentration and the content of TEOS used as cross-linking agent. The membrane containing 1 : 2 mass ratio of PVA and TEOS gave the highest separation selectivity of 1116 with a flux of 3.33 × 10^?2kg/m²h at 30°C for 10 mass% of water in the feed. Except for membrane M-1, the observed values of water flux are close to the values of total flux in the investigated composition range, signifying that the developed membranes are highly water selective. From the temperature dependence of diffusion and permeation values, the Arrhenius apparent activation parameters have been estimated. The resulting activation energy values obtained, showing that water permeation is lower than that of acetic acid, suggest that the membranes have higher separation efficiency. The activation energy values calculated for total permeation and water permeation are close to each other for all the membranes except membrane M-1, signifying that coupled-transport is minimal because of the higher selective nature of membranes. The negative heat of sorption values (ΔH _s) for water in all the membranes suggests a Langmuir mode of sorption.