Factors resisting protein adsorption on hydrophilic/hydrophobic self-assembled monolayers terminated with hydrophilic hydroxyl groups

The hydroxyl-terminated self-assembled monolayer(OH-SAM),as a surface resistant to protein adsorption,exhibits substantial potential in applications such as ship navigation and medical implants,and the appropriate strategies for designing anti-fouling surfaces are crucial.Here,we employ molecular dynamics simulations and alchemical free energy calculations to systematically analyze the factors influencing resistance to protein adsorption on the SAMs terminated with single or double OH groups at three packing densities(∑=2.0 nm^(-2),4.5 nm^(-2),and 6.5 nm^(-2)),respectively.For the first time,we observed that the compactness and order of interfacial water enhance its physical barrier effect,subsequently enhancing the resistance of SAM to protein adsorption.Notably,the spatial hindrance effect of SAM leads to the embedding of protein into SAM,resulting in a lack of resistance of SAM towards protein.Furthermore,the number of hydroxyl groups per unit area of double OH-terminated SAM at ∑=6.5 nm^(-2) is approximately 2 to 3 times that of single OH-terminated SAM at ∑=6.5 nm^(-2) and 4.5 nm^(-2),consequently yielding a weaker resistance of double OH-terminated SAM towards protein.Meanwhile,due to the structure of SAM itself,i.e.,the formation of a nearly perfect ice-like hydrogen bond structure,the SAM exhibits the weakest resistance towards protein.This study will complement and improve the mechanism of OH-SAM resistance to protein adsorption,especially the traditional barrier effect of interfacial water.

一维Sznajd舆论模型相变的研究

略去一维标准Szna jd舆论模型的第二个规则,修改后的模型演化的决定时间分布没有发生变化,但弛豫时间延长了;反铁磁性吸引子消失了,铁磁性终态吸引子出现的概率对初始态度人员密度有着重要的依赖关系.进一步在平均场的近似下,修改后的一维Szna jd舆论模型存在相变.

在开放边界条件下Nagel-Schreckenberg交通流模型的功率谱

在开放性边界条件下,从功率谱的角度讨论N age l-Schreckenberg随机交通流模型的相变,数值模拟结果充分地反映了交通流从自由流动相到拥堵相的相变,且在相变点上可以观察到1/f噪声信号.

提高水分子流出纳米碳管速度的特殊水分子偶极排布研究

使用分子动力学的方法,研究了水分子进出狭窄碳纳米管的过程.发现管口处水分子的偶极垂直于碳管时容易流出碳管.根据碳管中与之相邻的水分子的偶极方向可以把这种特殊构型分为2类.虽然,这2类特殊结构的出现概率非常小,但是它们对净流过碳管水分子的贡献与其它结构的贡献基本相同.这2种偶极排布中水分子比较接近管壁、远离Lennard-Jones势的平衡位置,导致这2种偶极排布中水分子能量升高,处于相对不稳定的状态,容易流出碳管.这个发现表明可以通过调控碳纳米管内的水分偶极方向控制管内的水分子流动.

Heterogeneous hydration patterns of G-quadruplex DNA

G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. Their structure and function are strongly influenced by their hydration shells. Although extensively studied through various experimental and computational methods, hydration patterns near DNA remain under debate due to the chemically and topologically heterogeneous nature of the exposed surface. In this work, we employed all-atom molecular dynamics(MD) simulation to study the hydration patterns of GQ DNA. The Drude oscillator model was used in MD simulation as a computationally efficient method for modeling electronic polarization in DNA ion solutions. Hydration structure was analyzed in terms of radial distribution functions and high-density three-dimensional hydration sites. Analysis of hydration dynamics focused on self-diffusion rates and orientation time correlation at different structural regions of GQ DNA.The results show highly heterogeneous hydration patterns in both structure and dynamics;for example, there are several insular high-density sites in the inner channel, and ‘spine of water’ in the groove. For water inside the loop, anomalous diffusion is present over a long time scale, but for water around the phosphate group and groove, diffusion becomes normal after ~30 ps. These essentially correspond to deeply buried structural water and strong interaction with DNA, respectively.

Water-Mediated Spontaneously Dynamic Oxygen Migration on Graphene Oxide with Structural Adaptivity for Biomolecule Adsorption

We theoretically and experimentally show that,with water being adsorbed,the graphene oxide(GO)is converted to a spontaneously dynamic covalent material under ambient conditions,where the dominated epoxy and hydroxyl groups are mediated by water molecules to spontaneously break/reform their C–O bonds to achieve dynamic oxygen migration.This dynamic material presents structural adaptivity for response to biomolecule adsorption.Both density functional theory calculations and ab initio molecular dynamics simulations demonstrate that this spontaneously dynamic characteristics is attributed to the adsorption of water molecules,which sharply reduces the barriers of these oxygen migration reactions on GO to the level less than or comparable to the hydrogen bonding energy in liquid water.

Influence of atomic force microscope(AFM) probe shape on adhesion force measured in humidity environment

In micro-manipulation, the adhesion force has very important influence on behaviors of micro-objects. Here, a theoretical study on the effects of humidity on the adhesion force is presented between atomic force microscope （AFM） tips and substrate. The analysis shows that the precise tip geometry plays a critical role on humidity depen- dence of the adhesion force, which is the dominant factor in manipulating micro-objects in AFM experiments. For a blunt （paraboloid） tip, the adhesion force versus humidity curves tends to the apparent contrast （peak-to-valley corrugation） with a broad range. This paper demonstrates that the abrupt change of the adhesion force has high correla- tion with probe curvatures, which is mediated by coordinates of solid-liquid-vapor contact lines （triple point） on the probe profiles. The study provides insights for further under- standing nanoscale adhesion forces and the way to choose probe shapes in manipulating micro-objects in AFM experiments.

The Gibbs-free-energy landscape for the solute association in nanoconfined aqueous solutions

The theoretical model and the numerical analyses on the Gibbs-free-energy of the association states of amphiphilic molecules in nanoconfined aqueous solutions are presented in detail. We exhibit the continuous change of the Gibbs-free-energy trend, which plays a critical role in the association states of the system transforming from the dispersion state, through the "reversible state", and finally to the aggregation state in amphiphilic molecule solutions. Furthermore, for the "reversible state", we present the difference in the free-energy barrier heights of the dispersion state and aggregation state, resulting from the competition between the entropy,which makes the solute molecules evenly disperse in the solution and the energy contribution driving the amphiphilic molecules to aggregate into a larger cluster. These findings provide a comprehensive understanding of confinement effects on the solute association processes in aqueous solutions and may further improve the techniques of material fabrication.

Comparisons of Criteria for Analyzing the Dynamical Association of Solutes in Aqueous Solutions

How to determine accurately the association states of solutes in aqueous systems is of fundamental importance in a variety of chemical, physical, and biological processes, We apply four widely used criteria to analyze the dynamic association processes of solutes, e.g., amphiphilic molecules, and to find the inappropriate selections of representative sites on solutes in these criteria may bring about appreciable influence on the estimation of dynamic association behaviors such as unrealistic packing radii and even misleading packing structures. It would be better to select dynamically representative sites on solute molecules based on the characteristic of solute associations. Our detailed discussions give a guide on how to determine an appropriate criterion to accurately analyze the association behaviors of solute molecules in aqueous solutions.

Determination of the vapor–liquid transition of square-well particles using a novel generalized-canonical-ensemble-based method

The square-well（SW） potential is one of the simplest pair potential models and its phase behavior has been clearly revealed, therefore it has become a benchmark for checking new theories or numerical methods. We introduce the generalized canonical ensemble（GCE） into the isobaric replica exchange Monte Carlo（REMC） algorithm to form a novel isobaric GCE-REMC method, and apply it to the study of vapor–liquid transition of SW particles. It is validated that this method can reproduce the vapor–liquid diagram of SW particles by comparing the estimated vapor–liquid binodals and the critical point with those from the literature. The notable advantage of this method is that the unstable vapor–liquid coexisting states,which cannot be detected using conventional sampling techniques, are accessed with a high sampling efficiency. Besides,the isobaric GCE-REMC method can visit all the possible states, including stable, metastable or unstable states during the phase transition over a wide pressure range, providing an effective pathway to understand complex phase transitions during the nucleation or crystallization process in physical or biological systems.

Gating of Water Flow Induced by Bending of a Carbon Nanotube

The ON-OFF state transition of the water transport induced by the structural bending of a carbon nanotube is studied by molecule dynamics simulation. The water permeation through a bent carbon nanotube shows excellent gating property with a threshold bending angle of about 14.6°. We also investigate the water density distribution inside the nanochannel to illustrate the mechanism.

Effect of interaction between loop bases and ions on stability of G-quadruplex DNA

G-quadruplexes(GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics(MD), and steered MD(SMD)simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions(K^(+)/Na^(+))is about the base stacking free energies indicates that there will be a competition among the binding of M^(+)-base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K+was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K+, such an interaction was unable to promote the stability of the loop with the sequence Cyt.

Orientations of special water dipoles that accelerate water molecules exiting from carbon nanotube

One-dimensional ordered water molecules entering and exiting from a carbon nanotube with an appropriate radius are studied with molecular dynamics simulations.It can be found that a water molecule near the nanotube end is more likely to be expelled from the nanotube if its dipole is almost perpendicular to the nanotube axis.The key to this observation is that those water molecules are closer to the wall of the nanotube away from the equilibrium position of the Lennar-Jones （LJ） potential.Thus,the interaction energy for those water molecules is relatively high.There are two particular structures of the perpendicular water molecule depending on the dipole direction of the adjacent water molecule in the nanotube.Although the probabilities of these structures are quite small,their contributions to the net flux across the nanotube end are approximately equal to the predominant structures.The present findings further show the possibility of controlling the water flow by regulating the dipole directions of the water molecules inside the nanochannels.

Concentration of nitrogen molecules needed by nitrogen nanobubbles existing in bulk water

This paper investigates the stability of nitrogen nanobubbles under dif~ ferent concentrations of nitrogen molecules by molecular dynamics simulations. It is found that the stability of nanobubbles is very sensitive to the concentration of nitrogen molecules in water. A sharp transition between disperse states and assemble states of nitrogen molecules is observed when the concentration of nitrogen molecules is changed. The relevant critical concentration of nitrogen molecules needed by the existing nitrogen nanobubbles is analyzed.

液态水微观结构研究的新进展

液态水有很多奇异特性.近年来,对液态水以何种微观结构形式存在的问题争议激烈.文章介绍了当前对水的微观结构的一些研究及其进展,讨论了液态水中的氢键模式与水的结构关系,进而用一个简化模型探讨了氢键的取向性与强弱性对水的异常行为的作用.

石墨烯和氧化石墨烯对细胞脂膜破坏作用研究

石墨烯作为一种新型材料不断受到关注,如何与生物分子(如蛋白质、细胞脂膜等)发生作用是其生物相容性方面的重要问题之一.石墨烯以sp2杂化的碳为主的成键方式,形成独特的二维结构,具有显著的疏水特征.细胞脂膜主要是由双亲的磷脂分子在水环境中自组装而成.早期实验组观察到石墨烯的抗菌现象,认为锋利的侧边可能会以类似于刀片的方式插入、切割细胞膜.在理论上,我们阐述了一种可能的石墨烯的细胞毒性的分子机理:石墨烯不仅会通过主动插入、切割细胞脂膜,而且会将大量的磷脂分子抽离细胞脂膜,从而破坏细胞膜的完整性导致细胞死亡;尽管氧化石墨烯表面分布着大量的亲水氧化基团,但氧化基团高关联分布特点致使氧化石墨烯有着类似的破坏细胞脂膜的能力.本文综述了石墨烯、氧化石墨烯纳米片与细胞脂膜相互作用的理论研究进展,着重阐述石墨烯和氧化石墨烯从细胞脂膜中大量地抽取磷脂分子的过程以及在此过程中环境水分子所起的关键作用.在石墨烯、氧化石墨烯和细胞脂膜的相互作用中所表现出的特点有可能是一种共性,也会出现在其他疏水特性的纳米材料(如纳米碳管、碳纳米线和大面积的富勒烯等)与细胞脂膜的相互作用过程中.

纳米限阈下的水分子作为载体的信号转换、传导和放大

通常各种信号处理器,如放大器、分流器等,都是利用电子或者光子进行信号的处理,当处理器小到纳米或分子尺度时,由于分子体系固有的复杂性,和来自热涨落和纳米尺度上区间信号的相互干扰等原因,分子层次上信号的准确传递、转换和放大常常是十分困难的.从分子层次的相互作用的角度来看,与静电相互作用的慢衰减方式和范德华作用的快速衰减方式相比,极性分子的偶极相互作用是屏蔽热噪声的影响且有效地避免分支信号间的干扰而实现分子层次上的长程信号传递的有效方法.本文回顾了如何利用限阈于特定管径的碳纳米管内的水分子单链有效地进行将单电子电量大小的电信号转换成偶极信号,并在常温热噪声的环境中实现有效地分子层次的长程信号传导,并进一步利用Y型水分子单链实现分子层次信号的放大.本文还讨论了Y型水分子单链实现分子层次信号放大的鲁棒性,并利用在水分子之外的极性小分子链——尿素分子链,再次展现这种通过偶极相互作用来实现分子层次的信息处理方式.对于人们设计新型的纳米信号传输器件、理解生物信号传递机制,这些研究具有重要的理论意义.

生物分子表面水的生物功能研究

生物分子表面的水在蛋白、核酸、生物膜结构的形成、稳定以及功能的实现中发挥着重要作用.半个多世纪以来,生物分子表面水如何参与生物过程的问题,持续引发关注.然而,目前为止对水分子如何具体发挥生物功能却仍然知之甚少.本文介绍了当前对生物分子表面水的微观结构和性质的一些研究及其进展,讨论了生物分子表面水的行为与实现生物功能的关系.最后,采用一个仿生表面的水行为,展现一个理解生物分子表面水以及生物分子表面水可能承载生物功能方面的新视角.

有限时间尺度内分子指向相关的不对称扩散研究

传统的经典扩散理论常常将分子和物体假设为球形,这些分子和物体的扩散是无偏移各向同性的。然而,当我们在纳米尺度去看分子和物体时,这些分子和物体呈现出各种不对称的结构。进一步,当我们观察的时间有限到小于几十纳秒时,我们会看到这些分子和物体的自由扩散表现出与它们的初始方位相关的特性。对于像甲醇分子这样的小分子,在约100 ps的有限时间内,常温下,不对称扩散能占到总扩散的10%左右。这样的不对称扩散丰富了分子的扩散理论,对生命和其他自然界现象的理解具有重要的意义,同时也可能提供一种通过控制分子的方向来驱动分子的方法。

Effects of Surface Dipole Lengths on Evaporation of Tiny Water Aggregation

Using molecular dynamics simulation, we compared evaporation behavior of a tiny amount of water molecules adsorbed on solid surfaces with different dipole lengths, including surface dipole lengths of 1 fold, 2 folds, 4 folds, 6 folds and 8 folds of 0.14 nm and different charges from 0.1e to 0.9e. Surfaces with short dipole lengths (1-fold system) can always maintain hydrophobic character and the evaporation speeds are not influenced, whether the surface charges are enhanced or weakened; but when surface dipole lengths get to 8 folds, surfaces become more hydrophilic as the surface charge increases, and the evaporation speeds increase gradually and monotonically. By tuning dipole lengths from 1-fold to 8-fold systems, we confirmed non-monotonic variation of the evaporation flux (first increases, then decreases) in 4 fold system with charges (0.1e-0.7e), reported in our previous paper [S. Wang, et al., J. Phys. Chem. B 116 (2012) 13863], and also show the process from the enhancement of this unexpected non-monotonic variation to its vanishment with surface dipole lengths increasing. Herein, we demonstrated two key factors to influence the evaporation flux of a tiny amount of water molecules adsorbed on solid surfaces: the exposed surficial area of water aggregation from where the water molecules can evaporate directly and the attraction potential from the substrate hindering the evaporation. In addition, more interestingly, we showed extra steric effect of surface dipoles on further increase of evaporation flux for 2-folds, 4-folds, 6-folds and 8-folds systems with charges around larger than 0.7e. (The steric effect is first reported by parts of our authors [C. Wang, et al., Sci. Rep. 2 (2012) 358]). This study presents a complete physical picture of the influence of surface dipole lengths on the evaporation behavior of the adsorbed tiny amount of water.