The physicochemical properties role of a functionalized alkyl-peptide in nanofibre formation and neural progenitor cells viability and survival

Amphiphilic alkyl-peptides as novel biomaterials form 3D scaffolds that are applicable in tissue engineering. Here, the nanofibre formation capability of a distinct alkyl-peptide was investigated using coarse-grained molecular dynamics simulation (CGMD) and experimental methods. The alkyl-peptide (Ace-FAQRVPPEEEGGGAAAAK-Nhe(C16)) was functionalized with a peptide epitope (FAQRVPPP) which can help to maintenance and differentiation of neural stem cells. Two alkyl-peptide systems were investigated: the all-functionalized system (with only bioactive alkyl-peptides) and the distributed system (a combination of bioactive and non-bioactive alkyl-peptides with ratio 1:2). The CGMD and TEM results confirm elongated nanofibres for all-functionalized system and cylindrical nanofibres for the distributed one. Furthermore, PC12 cells show a reliable growth on both 2D alkyl-peptides coated surfaces. Because of the nanofibres negative surface charges, the cell morphologies show clustered form in the distributed system and rounded shape in the all-functionalized one. Since the stem cell state preserves in cluster form, the physicochemical property of these nanofibres allows a potential advantage in stem cell long-time maintains.     

基于粗粒化模型对有机溶剂的分子动力学模拟

在基于Boltzmann分布对四种基本构象进行Monte Carlo取样后, 通过与全原子模型的范德华势比较得到了Gay-Berne (GB)参数. 又在对用量化计算得到的分子体系的电势进行电荷、偶极矩和四极矩的拟合后, 得到了电多极展开势(EMP)参数. 利用得到的粗粒化参数, 基于粗粒化模型, 对CHCl₃及四氢呋喃(THF)两种有机溶剂进行了分子动力学模拟(MDS), 并将结果同全原子模拟进行了比较. 计算结果表明用粗粒化模型从整体上能重复全原子模型的模拟结果, 但在某些细节的计算与全原子模型有偏差, 其原因可能是目前工作仅考虑了单位点情况, 为此今后在对具有复杂结构的分子进行粗粒化模拟时还应考虑合理放置及增加相互作用位点.     

高分子粗粒化分子动力学模拟进展

模拟与理论、实验相互补充,彼此验证,使我们在原子和分子尺度上理解相关实验现象中的微观物理机制。结合高性能计算机和计算技术的发展,模拟已发展成为独特的高分子科学研究手段,在高分子材料优化设计和性能与结构问的性能关系研究中起重要作用。高分子具有不同层次的结构,材料的性质和功能不仅取决于化学结构和分子性质,而且很大程度上取决...     

超支化聚合反应的多尺度模拟

超支化聚合物具有与树枝状大分子相似的物理和化学性质,其具有合成简单、分子量分布宽等突出特点,超支化聚合物分子的结构形成取决于聚合反应过程,本文介绍了超支化聚合反应模拟研究的最新进展.首先介绍了八位置键涨落粗粒化格子模型在超支化聚合反应模拟中的应用,该方法考虑了聚合物分子空间位阻效应、分子内成环和反应点活性等影响因素,从而可以模拟不同类型的超支化聚合反应;为了定量描述单体和聚合物分子结构,研究者进一步发展了杂化多尺度超支化聚合反应模拟方法,该方法通过玻尔兹曼反演迭代方法获取单体和聚合物特异性粗粒化力场,然后通过粗粒化分子动力学方法结合反应性Monte Carlo方法对特异性超支化聚合反应进行定量模拟.多尺度聚合反应模拟不仅可以精确计算超支化聚合物分子量、多分散性指数和支化度等一般性聚合物参数,还可以获取分子成环率、超支化大分子构象等重要分子结构信息,在超支化聚合反应基础研究与预测方面具有重要应用价值.     

小波变换软阈值去噪在粗晶材料超声检测中的应用

本研究多尺度小波分析方法在粗晶材料超声检测信号增强中的应用。在分析结构噪声，电噪声和缺陷信号的小波变换特性的基础上，提出一种用一个尺度间变化的门限闭值来抑制噪声的小波变换系数，并以各尺度缺陷信号的能量关系形成权值，加权重构信号来提高信噪比。实验结果表明，该方法具有很好的去噪效果，增强了粗晶材料缺陷的检出率。     

Coarse-grained potentials of single-walled carbon nanotubes

We develop the coarse-grained (CG) potentials of single-walled carbon nanotubes (SWCNTs) in CNT bundles and buckypaper for the study of the static and dynamic behaviors. The explicit expressions of the CG stretching, bending and torsion potentials for the nanotubes are obtained by the stick-spiral and the beam models, respectively. The non-bonded CG potentials between two different CG beads are derived from analytical results based on the cohesive energy between two parallel and crossing SWCNTs from the van der Waals interactions. We show that the CG model is applicable to large deformations of complex CNT systems by combining the bonded potentials with non-bonded potentials. Checking against full atom molecular dynamics calculations and our analytical results shows that the present CG potentials have high accuracy. The established CG potentials are used to study the mechanical properties of the CNT bundles and buckypaper efficiently at minor computational cost, which shows great potential for the design of micro- and nanomechanical devices and systems.     

Aggregation Behavior of Trisiloxane-Tailed Surface Active Ionic Liquids in Aqueous Solution: Coarse-Grained Molecular Dynamics Study

The aggregation behaviors of two trisiloxane-tailed surface active ionic liquids in water have been investigated by coarse-grained (CG) molecular dynamics simulation on the basis of MARTINI force field. The new CG model is developed from the optimized molecule computed by using density functional theory. Direct comparison of angles and bonds obtained from all-atom (AA) simulations with those calculated from the CG model has been conducted to validate the latter model. Excellent agreement between AA and CG demonstrates that the potential of the new CG model can represent the complex system well. The long time CG simulation has been performed to understand the formation process of micelles when dissolving ionic liquids in water. Vesicles were observed at the final stage of the simulation and their partially truncated views and density profiles were obtained to describe the structure in detail.     

Interactions between model inclusions on closed lipid bilayer membranes

Protein inclusions in the membranes of living cells interact via the deformations they impose on that membrane. Such membrane-mediated interactions lead to sorting and self-assembly of the inclusions, as well as to membrane remodelling, crucial for many biological processes. For the past decades, theory, numerical calculations and experiments have been using simplified models for proteins to gain quantitative insights into their behaviour. Despite challenges arising from nonlinearities in the equations, the multiple length scales involved and the nonadditive nature of the interactions, recent progress now enables for the first time a direct comparison between theoretical and numerical predictions and experiments. We review the current knowledge on the biologically most relevant case, inclusions on lipid membranes with a closed surface and discuss challenges and opportunities for further progress.     

PE/PEO/PE-PEO 对称三元共混体系相行为的耗散粒子动力学模拟研究

建立了对应实验体系聚乙烯/聚氧化乙烯/聚乙烯-聚氧化乙烯嵌段共聚物(PE/PEO/PE-PEO)的对称三元共混模型,并采用耗散粒子动力学(DPD)模拟方法对其相行为进行了理论研究.研究结果表明,随着均聚物体积分数的增加,体系的平衡相态发生由层状相(LAM)到双连续微乳液(BME)再到相分离(PS)的转变,相态演化规律和...     

Study of liquid crystal phases with a model soft ellipsoid contact potential

We propose a soft ellipsoid contact potential model (SECP) for a pair of identical uniaxial ellipsoidal molecules, considering the configuration dependent energy anisotropy explicitly along with their geometrical aspects. The present model is an extension of the ellipsoid contact potential (ECP), main contribution of which was to determine the correct contact function of the ellipsoidal core. Expressions for intermolecular forces and torques derived analytically from this new model pair interaction potential are presented hereto to make it useful for molecular dynamics simulation study. We also report on some observations of molecular dynamics simulation study to demonstrate the ability of this realistic coarse-grained potential in generating some important liquid crystal phases.