麋鹿朊蛋白结构稳定性的分子动力学研究

朊蛋白病是一种致命且具有高度传染性的神经退行性疾病.糜鹿是目前已经报道的哺乳类动物中较易发生朊蛋白病的物种之一.作者使用分子动力学和操控式分子动力学模拟相结合的方法对糜鹿正常朊蛋白的结构稳定性进行了研究.发现了麋鹿朊蛋白结构中的不稳定结构域分布以及热动力学性质,揭示了糜鹿朊蛋白稳定性的分子结构基础以及力学特征.     

IBIsCO: a molecular dynamics simulation package for coarse-grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.     

石墨烯/聚乙烯界面导热性能的分子动力学模拟

采用非平衡分子动力学模拟(NEMD)方法研究了石墨烯/聚乙烯纳米复合材料的界面导热性能,主要考察了石墨烯层数、尺寸对界面热阻的影响.研究结果表明:当石墨烯层数为一层时,界面热导为46.79 MW/(m~2K),随着石墨烯层数的增加,界面热导下降;但石墨烯层数超过四层后,界面热导趋于恒定接近39.00 MW/(m~2K);随着石墨烯尺寸的增大,石墨烯中较长波长声子被引发并对界面热传导起到主要的作用,最终导致界面热导逐渐增大.     

兔子朊蛋白结构稳定性的分子动力学研究(英文)

朊蛋白病是一种能够对人类和动物带来致命影响,并具有高度传染性的神经退行性疾病.兔子是目前已经报道的哺乳类动物中对朊蛋白病免疫的少数几个物种之一.我们将分子动力学和操控式分子动力学模拟相结合,研究了兔子正常朊蛋白的结构稳定性;同时讨论了蛋白结构的收敛性及刚性分布,并揭示了兔子朊蛋白中关键二级结构的动力学以及受力各向异性特征,证实了兔子朊蛋白结构的稳定性特征.     

A study on the structural transition of a single polymer chain by parallel tempering molecular dynamics simulation

The structural transition of a single polymer chain with chain length of 100,200 and 300 beads was investigated by parallel tempering MD simulation.Our simulation results can capture the structural change from random coil to orientationally ordered structure with decreasing temperature.The clear transition was observed on the curves of radius of gyration and global orientational order parameter P as the function of temperature,which demonstrated structural formation of a single polymer chain.The linear relationships between three components of square radius of gyration R_gx²,R_gx²,R_gz² and global orientational order P can be obtained under the structurally transformational process.The slope of the linear relationship between x（or y-axis） component R_gx²(or R_gy²) and P is negative,while that of RL as the function of P is positive.The absolute value of slope is proportional to the chain length.Once the single polymer chain takes the random coil or ordered configuration,the linear relationship is invalid.The conformational change was also analyzed on microscopic scale.The polymer chain can be treated as the construction of rigid stems connecting by flexible loops.The deviation from exponentially decreased behavior of stem length distribution becomes prominent,indicating a stiffening of the chain arises leading to more and more segments ending up in the trans state with decreasing temperature.The stem length N_tr is about 21 bonds indicating the polymer chain is ordered with the specific fold length.So,the simulation results,which show the prototype of a liquid-crystalline polymer chain,are helpful to understand the crystallization process of crystalline polymers.     

Local elevation: A method for improving the searching properties of molecular dynamics simulation

Summary The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.     

基于分子模拟技术煤焦分子模型构建

煤、焦是过程工业的重要原料。因此,有必要深入了解煤、焦分子结构以揭示其反应性。采用Materials Studio 7.0软件,从分子层次研究煤、焦的分子结构。根据已报道的文献,构建煤、焦的初始结构;基于分子力学原理对这些结构进行优化,使得模型物性与煤、焦物性相符;基于退火模拟算法对模型进行优化,从而使得模型密度、元素分析数据与真实值吻合;基于能量最小化原理,对煤、焦模型再次优化,从而获得其稳定、真实的分子构型。由计算结果发现,模型的估算密度、元素组成与已报道一致,说明构建的模型是有效、合理的;在模型优化过程中,相对于其他能量而言,库伦能和范德华能起着重要的作用。因此可以推断在煤、焦热加工过程中,弱键占据主要地位。另外,本文采用分子模拟技术构建煤、焦模型的方法对于构建其他复杂大分子结构有着重要的借鉴作用。     

Tetracyclines adsorption onto alumina: A comparative experimental and molecular dynamics simulation study

Using alumina (Al₂O₃) as the adsorbent, a static adsorption experiment was carried out in this study. It comprehensively evaluated the factors including Al₂O₃ dosage, adsorption temperature, and pH that influence the adsorption capability of three tetracyclines (TCs), namely, tetracycline hydrochloride (TC), chlortetracycline hydrochloride (CTC) and oxytetracycline hydrochloride (OTC). The results demonstrate that the adsorption efficiency increases with Al₂O₃ dosage. In addition, low-acid or natural solution is benefit for the adsorption. The adsorption behavior is more reasonably described with the Freundlich isotherm, and fits well with the pseudo-second-order kinetic model (R²?>?0.999). The results of molecular dynamics (MD) simulation show that the structures of TCs deformed during the combining process. The values of binding energy of TCs follow the order as: CTC (88.45?kcal/mol)?>?OTC (73.54?kcal/mol)?>?TC (54.28?kcal/mol). The MD simulation results agree well with the adsorption experimental results, which indicates that the MD simulation is reliable and reasonable. The MD simulation will provide theoretical knowledge in understanding the adsorption mechanism and environmental behavior of TCs.     

OOPSE: an object-oriented parallel simulation engine for molecular dynamics

OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.     

Structure and dynamics of water at water|Pt interface as seen by molecular dynamics computer simulation

Five molecular dynamics computer simulations were performed to study the structural and dynamical properties of water next to uncharged and charged Pt surfaces. The results show that the structure of a water layer adsorbed on the metal surface is very sensitive to the details of the water–metal potential. While patches of short-living hexagonal ice-like structure are observed in the adsorbed water layer next to the uncharged Pt(111) surface, a square lattice solid-like structure is seen for the layer on top of the uncharged Pt(100) surface. The orientational ordering for the following two layers of water next to uncharged Pt is displaying a preference towards the orientations that are characteristic of hexagonal ice-I, while water is liquid-like in these layers. In the presence of a high value external electric field water reorients and undergoes a layering transition.     

Non-adiabatic molecular dynamics simulation of ultrafast solar cell electron transfer

A non-adiabatic (NA) molecular dynamics (MD) simulation of the photoinduced electron transfer (ET) from a molecular electron donor to the TiO₂ acceptor is carried out. The system under study is typical of the dye sensitized semiconductor nanomaterials used in solar cells, photocatalysis and photoelectrolysis. The electronic structure of the dye-semiconductor system and the adiabatic dynamics are simulated by ab initio density functional theory MD, while the NA effects are incorporated by the quantum-classical mean-field approach. A novel procedure separating the NA and adiabatic ET pathways is developed. The simulation provides a detailed picture of the ET process. For the specific system under study, ET occurs on a 30 fs time scale, in agreement with the ultrafast experimental data. Both adiabatic and NA pathways for the ET are observed. The NA transfer entirely dominates at short times and can occur due to strong localized avoided crossing as well as extended regions of weaker NA coupling. Although the adiabatic ET contribution accumulates more slowly, it approaches that of the NA ET pathway asymptotically. The electron acceptor states are formed by the d-orbital of Ti atoms of the semiconductor and are localized within the first 3–4 layers of the surface. About 20% of the acceptor state density is localized on a single Ti atom of the first surface layer. The simulation predicts a complex non-single-exponential time dependence of the ET process.     

New all-atom force field for molecular dynamics simulation of an AlPO(4)-34 molecular sieve

A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of atomic charges. The average RMS difference between instantaneous positions of the framework atoms during 1 ns simulation and their positions in the structure determined from single crystal X-ray diffraction was calculated, and the average structure of the flexible framework was determined. The computed Debye-Waller factors and simulated FTIR spectra are in good agreement with the experimental data. The new force field permits detailed molecular dynamics simulations of flexible, charged aluminophosphate molecular sieves which should lead to a better understanding of the catalytic processes and the crucial role played by templating molecules.     

Internal coordinate density of state from molecular dynamics simulation

The vibrational density of states (DoS), calculated from the Fourier transform of the velocity autocorrelation function, provides profound information regarding the structure and dynamic behavior of a system. However, it is often difficult to identify the exact vibrational mode associated with a specific frequency if the DoS is determined based on velocities in Cartesian coordinates. Here, the DoS is determined based on velocities in internal coordinates, calculated from Cartesian atomic velocities using a generalized Wilson's B ‐matrix. The DoS in internal coordinates allows for the correct detection of free dihedral rotations that may be mistaken as hindered rotation in Cartesian DoS. Furthermore, the pronounced enhancement of low frequency modes in Cartesian DoS for macromolecules should be attributed to the coupling of dihedral and angle motions. The internal DoS, thus deconvolutes the internal motions and provides fruitful insights to the dynamic behaviors of a system. © 2015 Wiley Periodicals, Inc.     

Thermal characterization and kinetic analysis of nano‐ and micro‐Al/NiO thermites: Combined experimental and molecular dynamics simulation study

In the experimental part of this study, thermal properties of the Al and NiO composites in micro‐ and nano‐sized Al are investigated. Differential scanning calorimetry (DSC) analysis of the onset temperatures of ignition, activation energy (E_a), frequency factor (A), rate constant (k), critical ignition temperature of thermal explosion (T_b), and self‐accelerating decomposition temperature (T_SADT), as well as the thermodynamic parameters (ΔS^≠ , ΔH^≠ , and ΔG^≠ ) are used to explore the thermal behavior and analyze the kinetics. Thermal analysis suggests that the mechanism is based on solid–solid diffusion and liquid–gas for the nano‐ and micro‐Al/NiO composite, respectively. Our results indicate that the incorporation of nano‐Al particles can significantly reduce the ignition temperature, E_a, A, k, T_b, and T_SADT. In the second part of this work, molecular dynamics (MD) simulation is used to investigate the behavior of Al/NiO thermite reaction using the Reaxff force field to evaluate the experimental results. Theoretically, MD results show 1,154 K as the reaction ignition temperature, which is in reasonably good agreement with experimental temperature of 893°C (1,166 K). The radial distribution function (RDF) shows that no reaction occurs at 500 K but it is complete at 1,200 K.     

Solvation of xyloglucan in water/alcohol systems by molecular dynamics simulation

Xyloglucan in water solution turns into a gel with addition of alcohol such as methanol and ethanol. In regard to this phenomenon, we investigated the adhesive property of alcohol to xyloglucan and proposed the mechanism of the gelation by molecular dynamics (MD) simulation of a xyloglucan in water, water/methanol, and water/ethanol solution for 10 ns. The alcohol molecules showed its adhesive property to the xyloglucan and made the swelling-shrinking motion of the xyloglucan slow. Alcohol molecules solvated to the xyloglucan mainly in hydrophobic way so as to fill the void of water hydration shell, resulting in reformation of the hydrogen-bond network of water molecules around the solute. We also found that alcohol molecules have strong tendency to hydrogen-bond on xylose O3 in xyloglucan. According to these results, we proposed the gelation mechanism of xyloglucan in water/alcohol solution.     

Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

甲烷水合物导热机理的分子动力学模拟

甲烷水合物导热系数是甲烷水合物勘探、开采、储运以及其他应用过程中一个十分重要的物理参数.我们采用平衡分子动力学（EMD）方法Green-Kubo理论计算温度203.15～263.15K、压力范围3～100MPa、晶穴占有率为0～1的sI甲烷水合物的导热系数,采用的水分子模型包括TIP4P、TIP4P-Ew、TIP4P-FQ、TIP4P/2005、TIP4P/Ice.研究了主客体分子、外界温压条件等对甲烷水合物导热性能的影响.研究结果显示甲烷水合物的低导热性能由主体分子构建的sI笼型结构决定,而客体分子进入笼型结构后,使得笼型结构导热性能增强,同时进入笼型结构的客体分子越多,甲烷水合物导热性能越强.研究结果还显示在高温区域（T〉TDebye/3）内不同温度作用下,所有sI水合物具有相似的导热规律.压力对导热系数有一定影响,尤其是在较高压力条件下,压力越高,导热系数越大.而在不同温度和不同压力作用过程中,密度的改变对导热系数的增大或减小几乎没有影响.     

Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories

Subject of this work is the analysis of molecular dynamics (MD) trajectories of neurophysins I (NPI) and II (NPII) and their complexes with the neurophyseal nonapeptide hormones oxytocin (OT) and vasopresssin (VP), respectively, simulated in water. NPs serve in the neurosecretory granules as carrier proteins for the hormones before their release to the blood. The starting data consisted of two pairs of different trajectories for each of the (NPII/VP)2 and (NPI/OT)2 heterotetramers and two more trajectories for the NPII2 and NPI2 homodimers (six trajectories in total). Using essential dynamics which, to our judgement, is equivalent to factor analysis, we found that only about 10 degrees of freedom per trajectory are necessary and sufficient to describe in full the motions relevant for the function of the protein. This is consistent with these motions to explain about 90% of the total variance of the system. These principal degrees of freedom represent slow anharmonic motional modes, clearly pointing at distinguished mobility of the atoms involved in the protein's functionality.