非均匀外力对粗粒化DNA穿孔行为影响的模拟研究

通过建立DNA高分子的粗粒化模型,采用分子动力学方法模拟其穿孔行为,研究了不同的孔内非均匀外力对DNA高分子穿孔的影响.外力及高分子链内部势能在分子水平下对单体的综合作用很复杂,某些条件穿孔过程会产生后面粒子超过前面粒子而使高分子链堵塞在孔内的情况.研究还发现,穿孔行为是否成功与孔口力的大小有关,在成功穿孔的情况下,非均匀外力相比于恒力情况穿孔时间至少减少了1/2.这些结果对理解DNA复杂的穿孔机理提供了新的视角.     

基于Gay-Berne势能模型的粗粒化动力学模拟研究正丁醇的玻璃态相变

通过基于Gay-Berne势能模型的粗粒化动力学模拟,研究液态正丁醇体系的冷却过程. 采用密度泛函计算,拟合出适合正丁醇体系的GB势能参数. 体系的密度、平均势能等性质随温度的降低(由290 K降至50 K,间隔为10 K)发生特殊变化,即体系发生玻璃态相变,相变温度为T_g=120±10 K,与实验值110±1 K符合很好.     

粗粒化模型中的Gay-Berne相互作用势

合理描述非球形粗粒化粒子间的相互作用是提高粗粒化分子动力学模拟速度的关键.为此本文介绍了Gay-Berne势.将之应用于两种有机小分子体系,在合理选择构象集后,由遗传算法得到了粗粒化粒子的GB参数,并通过对粗粒化模型和全原子模型得到的范德瓦耳斯相互作用的对比检验了GB力场参数.最后,指出如何处理作用位点是粗粒化模型发展的一个关键问题.     

粗粒化自由能模拟研究ABC输出蛋白质构象态转变

本文应用了粗粒化分子动力学方法模拟计算了ATP结合盒式输出蛋白沿其构象转变途径反应坐标的平均力势,这个反应坐标被定义为内门和外门质量中心距离之差. 计算得到的平均力势能很好地描述不同的向内构象态、向外构象态和阻塞构象状态,以及它们之间的转变. 粗粒化分子动力学自由能模拟显示,在向内构象态到向外构象态转变过程中,内门在外门打开之前先行关闭;反之,在向外构象态到向内构象态转变过程中,外门在内门大开之前先行关闭. 因此,在向内构象态和向外构象态两种转变过程中,都经过了阻塞构象状态. 模拟结果揭示了ATP结合盒式输出蛋白的传输单向性,这种特性在生命体系功能实现中具有十分重要的意义. 这些结果与先前晶体结构实验［Proc. Natl. Acad. Sci. USA 104,19005 (2007)］发现有根本的不同,这些实验结果显示了内外门同时打开的不合理结果. 本文通过计算模拟阐明了ABC输出蛋白构象态变化的分子机理.     

随机反应扩散格气模型上钙动力学的粗粒化模拟

发展了一种基于随机格气模型的粗粒化方法,该方法能有效模拟内质网表面钙动力学信息. 首先将相邻的微观节点合并成粗粒化节点,再根据局域平均场近似推导出粗粒化反应速率,然后执行粗粒化动力学蒙特卡洛模拟. 发现粗粒化动力学蒙特卡洛模拟结果和微观模拟结果非常吻合. 有趣的是,存在一个最佳的粗粒化比m,使得粗粒化模拟与微观模拟的相变点偏差最小. 固定m,发现临界点随体系尺度增加而单调增加,而且相变点的偏差与体系尺度存在一个标度关系.此外,该粗粒化方法大大地加快了蒙特卡洛模拟速率,并且与微观模拟直接相关. 该方法可以广泛用来研究体系尺度效应,而节省大量计算时间.     

基于TorchMD的粗粒化分子动力模拟研究

粗粒化模型通过简化原子性质以及原子间的相互作用实现生物大分子长时间尺度的分子动力学模拟. 深度学习通过模拟人类的认知过程实现海量数据的准确分类和回归过程. 本论文将这两种技术进行融合,利用基于深度学习的粗粒化分子动力学模拟技术研究分子在不同状态之间的变化过程,并提出基于TorchMD的分子动力学模拟的分析框架. 在本工作中,MFDP聚类算法被用于在三维的CV变量空间中进行聚类,并确定分子的若干主要状态,在完成聚类的同时,给出各类中的代表分子构象,并给出类之间的分子构象. 这为后续利用String算法分析分子在不同状态间的转换路径打下基础. 通过String算法,迭代搜索得到分子在不同状态之间的变化路径以及对应的势能变化曲线. 通过与已有文献的结果进行对比,验证了基于TorchMD的粗粒化分子动力学模拟的理论框架可以在相对较短的时间尺度里研究分子的变化过程.     

网格上布鲁塞尔体系化学振荡的粗粒化模拟

将一种有效的粗粒化的动力学蒙特卡罗(KMC)方法用于加速模拟二维格气布鲁塞尔体系中的振荡行为．这种方法是将微观网格合并得到粗粒化的网格,并在该粗粒化网格上按粗粒化的反应速率执行KMC,即粗粒化的KMC．数值结果表明,由于非线性三分子反应导致的相邻元胞之间的关联是不能忽略的．通过正确的考虑这一边界效应,引入了所谓的b-LMF方法．大量的数据表明,只要体系的扩散系数不是很小,b-LMF方法能够很好的重现体系的振荡行为．另外,发现该方法所得的结果与KMC的偏离在合适的粗粒化尺度下存在一个接近于0的极小值,这一粗     

半晶态聚合物的分子动力学模拟

采用粗粒化聚乙烯醇模型,应用分子动力学方法模拟熔融态聚合物经过缓慢冷却、局部结晶形成半晶态聚合物的过程.静态结构因子的演变显示出在结晶初期小角散射强度的增大先于布拉格峰的出现,这与小角/大角X射线散射实验现象相一致.模拟得到的半晶态聚合物呈现为折叠链构成的晶区与非晶区交杂在一起的结构形态,与缨状微束结构模型相一致.研究发现在不同的冷却阶段具有不同的有序结构形成机制.从结晶温度到玻璃化温度的凝固过程中,存在分子链的伸展和伸直分子链之间平行排列两种形式的结构转变;而在玻璃化温度之后,材料的活性只允许调整伸直分子链之间的相对排列位置.     

冷却速度对Ga凝固过程的影响的模拟研究

采用分子动力学方法对Ga在相同初始状态下以不同速度冷却的凝固过程中进行了模拟研究。发现：以3.38×1013、3.38×1012K/s的速度冷却,得到非晶态结构;以2.01×1011K/s的速度冷却,发生明显晶化,结晶转变温度约为133K。这一结果,对于如何正确选择冷却速度获得优良材料性能,将具有重要的实际意义。     

冷速对液态金属Ga凝固过程中微观结构演变影响的模拟研究

采用分子动力学方法对液态金属Ga凝固过程中不同冷却速率对微观结构演变的影响进行了模拟跟踪研究. 运用HA键型指数法和原子成团类型指数法(CTIM)分析了金属原子Ga的成键类型和形成的基本原子团结构. 结果发现，冷却速率对凝固过程中的微观结构起着非常重要的作用. 在以1.0×10¹⁴，1.0×10¹³，1.0×10¹²K/s的速率冷却时，系统形成以与1311，1301键型相关的菱面体结构为主，夹杂着立方体、六角密集等其他团簇结构所构成的非晶态结构；在以1.0×10¹¹K/s的速率冷却时，系统明显发生结晶，其结晶转变温度T_c约为198K，且冷却速率越慢，结晶转变温度T_c越高，形成以与1421键型相关的斜方晶体(经可视化分析确认)为主要构型的晶态结构. 这将为研究液态金属的结晶转变过程提供一种新方法. 关键词： 液态金属Ga 凝固过程 微结构转变 分子动力学模拟     

Exploring the utility of coarse-grained water models for computational studies of interfacial systems

Molecular dynamics simulations have become a standard tool for the investigation of biological and soft matter systems. Water models serve as the basis of force fields used in molecular dynamics simulations of these systems. This article reports on an examination of the utility of a set of coarse-grained (CG) water models, with different resolutions, interaction potentials (Lennard–Jones, Morse), and cut-off distances. The relationships between the parameters under specific choices of the above options and the thermodynamic properties, such as density, surface tension, and compressibility, were found to fit simple mathematical equations. The limits of applicability of these CG water models were explored by checking the melting temperature. If a CG site is mapped to one or two real water molecules, a simple model with appropriate combinations of cut-off distances, functional forms, and parameters can be found to simultaneously match the experimental values of density, surface tension, and compressibility under ambient conditions. If more water molecules are included in a CG site, either the melting temperature approaches or surpasses room temperature, or the surface tension and compressibility cannot both be matched simultaneously. In striving for computational efficiency, it is still possible to find a simple CG water model with three water molecules contained in a CG bead that generates a liquid state of water with realistic values of density, surface tension and compressibility at ambient condition, but coarser models are not recommended.     

Comparative assessment of the ELBA coarse-grained model for water

The ELBA force field for water consists of a single spherical site embedded with a point dipole. This coarse-grained model is assessed here through the calculation of fundamental properties of bulk liquid water and the water–vapour interface. Accuracy and efficiency are evaluated and compared against simulations of standard three- and four-site atomistic models. For bulk liquid systems, ELBA reproduces accurately most of the investigated properties. However, the radial distribution function deviates from atomistic and experimental data, indicating a loss of local structure. The water–vapour interface, simulated over a range of temperatures from 300 to 600 K, is captured realistically in terms of its density distribution, and the accuracy in reproducing the experimental surface tension is as high as that of the best atomistic model. The critical temperature of ELBA is also found to be in excellent agreement with experiment. However, the interfacial electric field and surface potential are missing. The computational speed-up of ELBA compared to traditional atomistic models is estimated to be between one and two orders of magnitude.     

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

ABSTRACT

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.     

Role of surface ligands in nanoparticle permeation through a model membrane: a coarse-grained molecular dynamics simulations study

How nanoparticles interact with biological membranes is of significant importance in determining the toxicity of nanoparticles as well as their potential applications in phototherapy, imaging and gene/drug delivery. It has been shown that such interactions are often determined by nanoparticle physicochemical factors such as size, shape, hydrophobicity and surface charge density. Surface modification of the nanoparticle offers the possibility of creating site-specific carriers for both drug delivery and diagnostic purposes. In this work, we use coarse-grained molecular dynamic simulations to explore the permeation characteristics of ligand-coated nanoparticles through a model membrane. We compare permeation behaviors of ligand-coated nanoparticles with bare nanoparticles to provide insights into how the ligands affect the permeation process. A series of simulations is carried out to validate a coarse-grained model for nanoparticles and a lipid membrane system. The minimum driving force for nanoparticles to penetrate the membrane and the mechanism of nanoparticle–membrane interaction were investigated. The potential of the mean force profile, nanoparticle velocity profile, force profile and density profiles (planar and radial) were obtained to explore the nanoparticle permeation process. The structural properties of both nanoparticles and lipid membrane during the permeation, which are of considerable fundamental interest, are also studied in our work. The findings described in our work will lead to a better understanding of nanoparticle–lipid membrane interactions and cell cytotoxicity and help develop more efficient nanocarrier systems for intracellular delivery of therapeutics.     

Atomistic simulation of fcc-bcc phase transition in single crystal Al under uniform compression

By molecular dynamics simulations employing an embedded atom model potential,we investigate the fcc-to-bcc phase transition in single crystal Al,caused by uniform compression.Results show that the fcc structure is unstable when the pressure is over 250 GPa,in reasonable agreement with the calculated value through the density functional theory.The morphology evolution of the structural transition and the corresponding transition mechanism are analysed in detail.The bcc (011) planes are transited from the fcc (11) plane and the (11) plane.We suggest that the transition mechanism consists mainly of compression,shear,slid and rotation of the lattice.In addition,our radial distribution function analysis explicitly indicates the phase transition of Al from fcc phase to bcc structure.     

Comparison of modern Langevin integrators for simulations of coarse-grained polymer melts

For a wide range of phenomena, current computational ability does not always allow for atomistic simulations of high-dimensional molecular systems to reach time scales of interest. Coarse-graining (CG) is an established approach to alleviate the impact of computational limits while retaining the same algorithms used in atomistic simulations. It is important to understand how algorithms such as Langevin integrators perform on non-trivial CG molecular systems, and in particular how large of an integration time step can be used without introducing unacceptable amounts of error into averaged quantities of interest. To investigate this, we examined three different Langevin integrators on a CG polymer melt: the recently developed BAOAB method by Leimkuhler and Matthews [J. Chem. Phys. 138 (17), 05B601_1 (2013)], the Grønbech-Jensen and Farago method [Mol. Phys. 111 (8), 983-991 (2013)], or G-JF, and the frequently used Brünger–Brooks–Karplus integrator [Chem. Phys. Lett. 105 (5), 495-500 (1984)], known as BBK. We compute and analyse key statistical properties for each. Our results indicate that the integrators perform similarly for a small friction parameter; however outside this regime, the use of large integration steps produces significant deviations from the predicted diffusivity and steady-state distributions for all methods examined with the exception of G-JF.     

Atomistic simulation of fccben bcc phase transition in single crystal Al under uniform compression

By molecular dynamics simulations employing an embedded atom model potential, we investigate the fcc-to-bcc phase transition in single crystal Al, caused by uniform compression. Results show that the fcc structure is unstable when the pressure is over 250 GPa, in reasonable agreement with the calculated value through the density functional theory. The morphology evolution of the structural transition and the corresponding transition mechanism are analysed in detail. The bcc (011) planes are transited from the fcc (111) plane and the (111) plane. We suggest that the transition mechanism consists mainly of compression, shear, slid and rotation of the lattice. In addition, our radial distribution function analysis explicitly indicates the phase transition of Al from fcc phase to bcc structure.     

Ti75Al25合金微观结构演变的分子动力学模拟

本文利用分子动力学模拟方法, 研究了液态Ti75Al25合金在不同冷却条件下形成晶体及非晶的过程(Q1:1.0×1013 Ks-1, Q2: 1.0×1011 Ks-1). 利用平均原子体积、双体分布函数、键角分布函数、键对分析和Voronoi多面体方法研究了微观局域结构随温度的变化关系. 研究发现：在Q1冷却过程中,液态Ti75Al25合金在1000 K发生玻璃化转变,形成非晶结构; 而在Q2冷却过程中,液态Ti75Al25合金发生结晶,并最终形成hcp晶体结构。     

Ti75Al25合金微观结构演变的分子动力学模拟

本文利用分子动力学模拟方法,研究了液态Ti₇₅Al₂₅合金在不同冷却条件下形成晶体及非晶的过程(Q1:1.0×10¹³K Ks^-1,Q2:1.0×10¹¹Ks^-1).利用平均原子体积、双体分布函数、键角分布函数、键对分析和Voronoi多面体方法研究了微观局域结构随温度的变化关系.研究发现:在Q1冷却过程中,液态Ti₇₅A1₂₅合金在1000 K发生玻璃化转变,形成非晶结构;而在Q2冷却过程中,液态Ti₇₅Al₂₅合金发生结晶,并最终形成hcp晶体结构.