Dynamic mechanism of HIV replication inhibitor peptide encapsulated into carbon nanotubes

Biomolecules encapsulated in carbon nanotubes (CNTs) have attracted much interest and facilitated exciting opportunities for biological and biomedical applications of CNTs. Understanding the fundamental interaction and change in biomolecules during encapsulation is indispensable but remains a challenge for both theoretical and experimental investigations. This paper focuses on the interaction between HIV replication inhibitor peptide (HRIP) and CNTs in a neutral solution with molecular dynamics simulation. We observed that HRIP spontaneously inserts into the CNTs and oscillates around the center of the tube, where the non-covalent interaction is minimum. The effects of the diameters of the CNTs on HRIP were investigated. The optimal diameter of the CNT that can provide the most effective encapsulation and causes minimum conformational change in HRIP was found. The present results provide valuable insights in the understanding of nanoscale drug delivery using CNT-based devices.     

I50V变异对HIV-1蛋白酶抑制剂Amprenavir抗药机制的分子动力学研究

HIV-1蛋白酶PR(HIV-1 protease)的变异对抑制剂产生抗药性,严重消弱抗艾滋病的治疗效果.I50V变异是HIV-1蛋白酶残基变异中最重要的一个.采用分子动力学模拟和溶解相互作用能方法SIE(solvated interaction energy)研究I50V变异对抑制剂APV(amprenavir)抗药机制.分子动力学分析表明I50V变异诱导HIV-1蛋白酶整体柔性的增加,影响了抑制剂与蛋白酶的相互作用.结合自由能计算表明范德华作用的下降驱动了I50V变异对APV的抗药性.基于残基的能量分解证明V50/V50'与APV的相互作用相对于野生型的I50/I50'明显减弱,诱导了抗药性.本研究能为高效的缓解抗药性抑制剂的研发提供一定的理论指导.     

稀有气体原子在纳米碳管中的周期性振荡

采用TLHT势和经典分子动力学方法研究了稀有气体原子进入单壁纳米碳管(SWCNT)的动力学过程，计算得出SWCNT能吸入稀有气体原子(He，Ne，Ar，Kr，Xe)的管径阈值r₀分别为6.3 ?，7.0 ?，8.6 ?，8.6 ?，8.6 ?，同时计算了对应的每种稀有气体原子能封装在不同管径的SWCNT中的最大初始动能E_k0.计算给出有趣的结果是封装在纳米碳管中的稀有气体原子在管中不停地作周期性振荡，振荡周期与原子进入管中的能量无关，振幅与原子进入管中的能量有关，即振幅随着入射能量的增加而增加.分析表明：给定合适类型的碳管，具有很小初始动能的稀有气体原子可在碳管中稳定的周期性振荡，其振荡频率可达GHz.     

Structure of Lennard–Jones nanowires encapsulated by carbon nanotubes

Molecular dynamics simulations have been performed to investigate the structures of Lennard–Jones(LJ) nanowires(NWs) encapsulated in carbon nanotubes(CNTs). We find that the structures of NWs in a small CNT only adopt multi-shell motifs, while the structures of NWs in a larger CNT tend to adopt various motifs. Among these structures, three of them have not been reported previously. The phase boundaries among these structures are obtained regarding filling fractions, as well as the interaction between NWs and CNTs.     

Anisotropic formation mechanism and nanomechanics for the self-assembly process of cross-β peptides

Nanostructures self-assembled by cross-β peptides with ordered structures and advantageous mechanical properties have many potential applications in biomaterials and nanotechnologies. Quantifying the intra-and inter-molecular driving forces for peptide self-assembly at the atomistic level is essential for understanding the formation mechanism and nanomechanics of various morphologies of self-assembled peptides. We investigate the thermodynamics of the intra-and inter-sheet structure formations in the self-assembly process of cross-β peptide KIIIIK by means of steered molecular dynamics simulation combined with umbrella sampling. It is found that the mechanical properties of the intra-and inter-sheet structures are highly anisotropic with their intermolecular bond stiffness at the temperature of 300 K being 5.58 N/m and0.32 N/m, respectively. This mechanical anisotropy comes from the fact that the intra-sheet structure is stabilized by enthalpy but the inter-sheet structure is stabilized by entropy. Moreover, the formation process of KIIIIK intra-sheet structure is cooperatively driven by the van der Waals(VDW) interaction between the hydrophobic side chains and the electrostatic interaction between the hydrophilic backbones, but that of the inter-sheet structure is primarily driven by the VDW interaction between the hydrophobic side chains. Although only peptide KIIIIK is studied, the qualitative conclusions on the formation mechanism should also apply to other cross-β peptides.     

基于原子运动模型的类金刚石薄膜生长机理研究

利用分子动力学模拟方法，从原子尺度上研究了类金刚石(DLC)薄膜生长过程. 按照运动特点把入射原子在表面的行为分为表面冷冻、迁移、注入和反弹等四种，并由此提出原子运动模型. 入射原子的表面行为对DLC薄膜的微观结构以及生长方式有重要影响. 其中原子水平迁移是薄膜热弛豫的主要途径，入射原子的注入和迁移行为相互竞争，决定了薄膜生长的模式和最终结构. 利用统计分析手段给出了入射能量对原子表面行为进而对薄膜结构的影响，加深了对DLC薄膜生长机理的认识.     

硅纳米颗粒在碳纳米管表面生长的分子动力学模拟

采用分子动力学模拟方法研究了硅纳米颗粒在碳纳米管上的生长，并分析了这种复合材料的基本结构.研究表明，由于硅原子和碳纳米管之间的相互作用以及碳纳米管的巨大的表面曲率，硅原子在碳纳米管表面不是形成覆盖碳纳米管的二维薄膜，而是生成具有三维结构的硅纳米颗粒.小纳米颗粒的结构和无基底条件下生成的颗粒结构基本一致.对于大纳米颗粒，不同于无基底条件下形成的球状纳米晶体硅结构，硅纳米颗粒沿管轴方向伸长，其结构为类似于硅晶体的无定形网络结构. 关键词： 纳米颗粒 碳纳米管 硅 分子动力学模拟     

Influence of chirality on the thermal conductivity of single-walled carbon nanotubes

The influence of chirality on the thermal conductivity of single-walled carbon nanotubes(SWNTs) is discussed in this paper, using a non-equilibrium molecular dynamics(NEMD) method. The tube lengths of the SWNTs studied here are 20, 50, and 100 nm, respectively, and at each length the relationship between chiral angle and thermal conductivity of a SWNT is revealed. We find that if the tube length is relatively short, the influence of chirality on the thermal conductivity of a SWNT is more obvious and that a SWNT with a larger chiral angle has a greater thermal conductivity. Moreover, the thermal conductivity of a zigzag SWNT is smaller than that of an armchair one. As the tube length becomes longer, the thermal conductivity increases while the influence of chirality on the thermal conductivity decreases.     

Thermal conductivity of multi-walled carbon nanotubes:Molecular dynamics simulations

Heat conduction in single-walled carbon nanotubes(SWCNTs) has been investigated by using various methods, while less work has been focused on multi-walled carbon nanotubes(MWCNTs). The thermal conductivities of the double-walled carbon nanotubes(DWCNTs) with two different temperature control methods are studied by using molecular dynamics(MD) simulations. One case is that the heat baths(HBs) are imposed only on the outer wall, while the other is that the HBs are imposed on both the two walls. The results show that the ratio of the thermal conductivity of DWCNTs in the first case to that in the second case is inversely proportional to the ratio of the cross-sectional area of the DWCNT to that of its outer wall. In order to interpret the results and explore the heat conduction mechanisms, the inter-wall thermal transport of DWCNTs is simulated. Analyses of the temperature profiles of a DWCNT and its two walls in the two cases and the interwall thermal resistance show that in the first case heat is almost transported only along the outer wall, while in the second case a DWCNT behaves like parallel heat transport channels in which heat is transported along each wall independently.This gives a good explanation of our results and presents the heat conduction mechanisms of MWCNTs.     

碳纳米管包裹的硅纳米线复合结构的热稳定性研究

采用经典分子动力学方法模拟一定直径[111]晶向的硅纳米线填充不同扶手椅型单壁碳纳米管复合结构的加热过程, 通过可视化和能量分析的方法判断复合结构中硅纳米线和碳纳米管的热稳定性. 通过讨论碳纳米管的空间限制作用和分子间相互作用力的关系, 对碳纳米管和硅纳米线的热稳定性变化进行初步解释. 研究发现碳纳米管中硅纳米线的热稳定性和碳纳米管的直径关系密切: 当管径较小时, 硅纳米线的热稳定性有所提高, 当管径增大到一定大小时, 硅纳米线的热稳定性会突然显著地下降, 直到硅纳米线与管壁不存在分子间相互作用力, 硅纳米线的热稳定性才会恢复. 而硅纳米线填充到碳纳米管中对碳纳米管的热稳定性有着明显的降低作用.     

液体水银在碳纳米管中传输的压力控制模型

碳纳米管在纳米技术中有一个很重要的应用,就是它可以作为纳米管道传输液体. 本文用分子动力学模拟方法,结合一个液体压力控制模型,对液体水银由于外部压力作用在碳纳米管中传输的现象进行研究. 研究结果表明,当液体水银的内部压强超过一个临界值时,液体水银能够浸入到碳纳米管内部;不断增大液体内部的压强,碳纳米管可以连续地传输液体;而当对液体水银进行循环加压时,碳纳米管可以间断地传输液体水银. 关键词： 碳纳米管 流体传输 分子动力学     

液体水银在碳纳米管中传输的压力控制模型

碳纳米管在纳米技术中有一个很重要的应用，就是它可以作为纳米管道传输液体. 本文用分子动力学模拟方法，结合一个液体压力控制模型，对液体水银由于外部压力作用在碳纳米管中传输的现象进行研究. 研究结果表明，当液体水银的内部压强超过一个临界值时，液体水银能够浸入到碳纳米管内部；不断增大液体内部的压强，碳纳米管可以连续地传输液体；而当对液体水银进行循环加压时，碳纳米管可以间断地传输液体水银.     

电场引发的嵌有碳纳米管的黑索金复合材料分解模拟

以电场作为引燃条件对含能材料的分解过程进行了研究。利用黑索金(RDX)单晶结构，构建了镶嵌有碳纳米管(CNT)的黑索金(RDX)复合结构模型，利用反应分子动力学模拟研究了该材料在外电场下的响应。结果表明构建的复合结构在方向沿CNT 的匀强电场下，能够以CNT 为中心形成反应热点；随着热点的成长，形成了自发行进的燃烧层，可以分解掉整个体系。     

含氢碳膜的生长机制: 分子动力学模拟研究低能量CH基团的作用

探索等离子增强化学气相沉积(PECVD)技术中含氢碳膜的生长机理, 制备出常态超润滑含氢碳膜是表面工程技术领域的目标之一. 基于REBO势函数, 采用分子动力学模拟方法, 通过对比研究CH基团在清洁金刚石和吸氢金刚石表面的沉积行为, 发现低能量CH基团在清洁金刚石(111)面上的吸附效率大于98%, 而在吸氢金刚石(111)面上的吸附效率低于1%. 结果表明PECVD法制备含氢碳膜时, 低能量CH基团对薄膜生长的贡献主要来自于其在表面非饱和C位置的选择性吸附.     

Thermal conductivity and diffusion behaviour of lauric acid confined in carbon nanotubes as heat storage materials

The thermal conductivity and diffusion behaviour of lauric acid (LA) confined in single-walled carbon nanotube (CNT) with the filling ratio of 80% are investigated by molecular dynamics (MD) simulations. It is found that the concentric multilayer LA tubes are clearly observed under the interaction of CNT and LA and the hydrogen bonds (HB) among LA molecules in a confined environment. Due to the phonon scattering in low-frequency and the high-thermal conductivity characteristics of CNT, the axial thermal conductivity of CNT/LA is 49–57% lower than that of empty CNT and 115–188 times higher than that of crystal LA at the temperature range of 280 and 360?K. The confined LA molecules move as a whole cluster due to the long-lasting HB action and travel much faster than the bulk.     

Rayleigh-Ritz axial buckling analysis of single-walled carbon nanotubes with different boundary conditions

Eringen's nonlocality is incorporated into the shell theory to include the small-scale effects on the axial buckling of single-walled carbon nanotubes (SWCNTs) with arbitrary boundary conditions. To this end, the Rayleigh-Ritz solution technique is implemented in conjunction with the set of beam functions as modal displacement functions. Then, molecular dynamics simulations are employed to obtain the critical buckling loads of armchair and zigzag SWCNTs, the results of which are matched with those of nonlocal shell model to extract the appropriate values of nonlocal parameter. It is found that in contrast to the chirality, boundary conditions have a considerable influence on the proper values of nonlocal parameter.     

MDM2与抑制剂PDIQ作用机制的结合自由能计算研究

p53-MDM2之间的相互作用是抗癌药物设计的重要靶标。采用分子动力学模拟和结合自由能计算研究抑制剂PDIQ与MDM2的结合模式,结果显示范德华作用是二者结合的主体力量。基于残基的自由能分解计算结果表明CH-CH、CH-π和π-π相互作用驱动了二者的结合。这一研究成果可为抗癌药物的设计提供理论上的指导。     

A mechanism for cutting carbon nanotubes with a scanning tunneling microscope

We discuss the local cutting of single-walled carbon nanotubes by a voltage pulse to the tip of a scanning tunneling microscope. The tip voltage ( V) is the key physical quantity in the cutting process. After reviewing several possible physical mechanisms we conclude that the cutting process relies on the weakening of the carbon-carbon bonds through a combination of localized particle-hole excitations induced by inelastically tunneling electrons and elastic deformation due to the electric field between tip and sample. The carbon network releases part of the induced mechanical stress by forming topological defects that act as nucleation centers for the formation of dislocations that dynamically propagate towards bond-breaking. Received 6 April 2000     

Vibrations of single- and double-walled carbon nanotubes with layerwise boundary conditions: A molecular dynamics study

In the present work, the vibration characteristics of single- and double-walled carbon nanotubes under various layerwise boundary conditions at different lengths are investigated. This is accomplished by the use of molecular dynamics simulations based on the Tersoff-Brenner and Lennard-Jones potential energy functions. The effects of initial tensile and compressive strains on the resonant frequency of carbon nanotubes are also taken into consideration. From the results generated, it is observed that the natural frequency of carbon nanotubes is strongly dependent on their boundary conditions especially when tubes are shorter in length. The natural frequency and its dependence on tube end conditions reduce by increasing the tube length. The natural frequency of DWCNTs lies between those of the constituent inner and outer SWCNTs and is nearer to those of the outer one. It is further observed that the natural frequency is highly sensitive to tensile and compressive strains. The frequency shift occurring in the presence of small initial strains is positive for tensile strains and negative for compressive strains. The results obtained provide valuable information for calibrating the small scaling parameter of the nonlocal models for the vibration problem of carbon nanotubes.     

抑制剂Benzamidine与胰岛素作用机制的分子动力学和结合自由能计算研究

氢键和极性相互作用在抑制剂-蛋白结合专一性识别过程中起到重要作用. 抑制剂Benzamidine(BEN)与胰岛素trypsin相互作用机制的阐明有助于胰岛素高效抑制剂的研发.本文采用分子动力学模拟和MM-PBSA(molecular mechanics-Poisson Boltzmann surface area)从原子层次上研究BEN与胰岛素的结合模式.结果表明抑制剂BEN的脒基不仅与Asp189的羰基产生静电相互作用，而且与残基Ser190和Gly214形成氢键相互作用.基于残基能量分解的计算表明抑制剂的苯基与残基His58, Cys191, Gln192, Trp211, Gly212和Cys215形成有利于抑制剂结合的疏水性相互作用.期望当前的研究能为胰岛素有效抑制剂的研发提供重要的理论指导.