高压下钙钛矿结构MgSiO3的分子动力学研究

利用分子动力学方法,研究了高温高压下钙钛矿结构MgSiO3的状态方程.研究表明,分子动力学模拟结果很好地再现了广泛温度和压强范围内钙钛矿结构MgSiO3的摩尔体积.温度300 K压强上升到120 GPa模拟的钙钛矿结构MgSiO3状态方程和有效的实验结果基本一致.在更高温度和更高压强下模拟的钙钛矿结构MgSiO3状态方程和他人的计算值吻合的很好.另外,还分别计算了温度300 K,900 K,1500 K和2500 K压强上升到120 GPa时MgSiO3的体积压缩率.     

CaF2熔化温度的分子动力学模拟

利用壳层模型分子动力学方法,研究了高温高压条件下CaF2的熔化温度,同时计算了温度为300K、压强上升到100GPa时CaF2 的状态方程.研究中考虑了分子动力学模拟的过热熔化,通过晶体的现代熔化理论,对CaF2 的分子动力学模拟熔化温度进行了修正, 获得了高温高压下CaF2的熔化温度.因此,常压下壳层模型分子动力学方法为研究物质熔化提供了一个很好的方法.     

MgSiO3状态方程的分子动力学模拟

利用分子动力学方法,研究了高温高压下钙钛矿结构MgSiO_3的状态方程。研究表明,分子动力学模拟结果精确地再现了广泛温度和压强范围内MgSiO_3的摩尔体积。在300 K压强上升到140 GPa模拟的MgSiO_3状态方程和有效的实验值、他人的拟合值以及基于局域密度近似的第一原理计算结果基本一致。并且更高温度和更高压强下模拟的MgSiO_3状态方程和他人的计算值吻合的很好。另外,还分别计算了300、900、2000和3000 K压强上升到120 GPa时MgSiO_3的体积压缩率。     

壳层模型分子动力学在CaO研究中的应用

利用壳层分子动力学方法结合有效的对势,研究了高压条件下CaO的熔化曲线。研究表明,分子动力学模拟结果精确地再现了广泛压强范围内CaO的状态方程。研究中考虑了分子动力学模拟熔化存在的过热现象,通过晶体的现代熔化理论,对CaO的分子动力学模拟熔化温度进行了修正,获得了高温高压下CaO正确的熔化温度。因此,常压下引入壳层模型的分子动力学为研究物质熔化提供了一个很好的方法,这种方法可进一步推广到其它物质的高压熔化研究中。     

微通道中水蒸气凝结过程流型变化的分子动力学研究

本文建立了外力作用下流体流动和凝结过程的分子动力学模型.在蒸汽压力为3.7177 MPa时,模拟得到了不同外力条件下水蒸气凝结过程的流型,分别为环状流、射状流、塞状流、泡状流、带有小汽泡的液体流,模拟结果与相关文献中实验流型吻合较好.模拟发现水蒸气在0.3833 MPa压力下凝结时,出现一种新的波动流流型.最后对凝结过程中流型间转换机理进行了讨论.     

下地幔条件下钙钛矿结构MgSiO3熔化行为的研究

利用分子动力学方法结合有效的对势,模拟了下地幔条件下钙钛矿结构MgSiO3的熔化曲线．研究表明,分子动力学模拟结果精确地再现了广泛压强范围内钙钛矿结构MgSiO3的状态方程,并且熔化曲线与最新的实验结果也符合的很好．在压强上升到下地幔压强范围内,压强低于60 GPa时的钙钛矿结构MgSiO3熔化曲线比较陡,接着变得平缓．在核幔边界压强135 GPa时,钙钛矿结构MgSiO3的熔化温度是6500 K,明显低于Zerr和Boehler实验结果的外推结果．     

超高压水的分子动力学模拟

 采用平衡分子动力学（EMD）方法,模拟研究了温度范围为243~348 K、压强范围为0.1~400 MPa条件下水的热力学性质、结构和动力学性质,模拟结果与实验值吻合较好。模拟结果表明,随着压强的增大,水分子间的氢键作用增强,扩散系数减小;随着温度的升高,水分子间的氢键作用减弱,有序程度下降,扩散系数增大。但在过冷水中,扩散系数随压强的增大有增加的趋势。     

高压处理后大豆分离蛋白溶解性和流变特性的变化及其机理

 对高压处理后大豆分离蛋白溶解性和流变特性的变化及其机理进行了研究。经400 MPa、15 min高压处理使低浓度大豆分离蛋白溶液中蛋白质溶解性的提高最为显著。高压处理使大豆分离蛋白溶液的表观粘度增加,其贮藏模量G'和损耗模量G'也随着处理压力的提高而增大。扫描电镜观察和凝胶电泳的结果都显示,在低于400 MPa高压处理后大豆分离蛋白分子发生一定程度的解聚和伸展,蛋白质颗粒减小,溶液中蛋白质的体积分数增加。而红外光谱分析表明,高压处理后蛋白质电荷分布加强。高压处理后大豆分离蛋白分子结构上的改变是导致其有关理化性质变化的原因。     

基于接触数引导的迭代多组独立分子动力学模拟实现配体-蛋白质结合与解离过程

配体的结合与解离过程在蛋白质实现其生物学功能方面非常关键,因此对这些高度动态过程的研究变得非常重要. 尽管已有实验方法可以确定蛋白质-配体复合物的三维结构,但一般仅可获得静态图片. 随着计算机算力的快速提高以及算法的优化,分子动力学模拟在探索配体的结合与解离过程方面具有诸多优势. 然而,当系统变得足够大时,分子动力学模拟的时间和空间尺度成为了巨大的挑战. 本工作提出了一种研究配体-蛋白质结合与解离的增强采样工具,它基于配体和蛋白质之间形成的接触数来引导迭代多组独立分子动力学模拟. 在腺苷酸激酶的模拟结果中,观测到配体的结合和解离过程,而使用传统分子动力学模拟在同一时间尺度下则无法实现这一过程.     

近饱和区过热水蒸汽性质的分子动力学模拟研究

本文根据统计热力学理论,应用分子动力学模拟方法,对过热水蒸气的热物性进行了研究.选取实验压力为10MPa,利用TIP4P模型和不同经典方程,模拟计算温度从320℃到800℃时水蒸气的压力.从结果可以看出:近饱和区标准维里方程模拟压力值偏离实验值较远,径向状态方程和段式状态方程模拟结果的误差要小于维里方程的.随温度的增加,三种方程的模拟结果均趋于实验值.另外,本文还对影响模拟结果的一些因素进行了详细的讨论.     

Protein folding kinetics and thermodynamics from atomistic simulations

Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled in some manner, as, for example, in the replica exchange MD method. Here we present results obtained with a new analysis tool that allows the deduction of faithful kinetics data from a heterogeneous ensemble of simulation trajectories. The method is demonstrated on the decapeptide Chignolin for which we predict folding and unfolding time constants of 1.0 +/- 0.3 and 2.6 +/- 0.4 micros, respectively. We also derive the energetics of folding, and calculate a realistic melting curve for Chignolin.     

A network of conformational transitions in an unfolding process of HP-35 revealed by high-temperature MD simulation and a Markov state model

An understanding of protein folding/unfolding processes has important implications for all biological processes, including protein degradation, protein translocation, aging, and diseases. All-atom molecular dynamics(MD) simulations are uniquely suitable for it because of their atomic level resolution and accuracy. However, limited by computational capabilities, nowadays even for small and fast-folding proteins, all-atom MD simulations of protein folding still presents a great challenge. An alternative way is to study unfolding process using MD simulations at high temperature. High temperature provides more energy to overcome energetic barriers to unfolding, and information obtained from studying unfolding can shed light on the mechanism of folding. In the present study, a 1000-ns MD simulation at high temperature(500 K)was performed to investigate the unfolding process of a small protein, chicken villin headpiece(HP-35). To infer the folding mechanism, a Markov state model was also built from our simulation, which maps out six macrostates during the folding/unfolding process as well as critical transitions between them, revealing the folding mechanism unambiguously.     

Application of shell model in molecular dynamics simulation to MgO

The P－V－T equation of state of MgO has been simulated under high pressure and elevated temperature using the molecular dynamics (MD) method with the breathing shell model (BSM). It is found that the MD simulation with BSM is very successful in reproducing accurately the measured molar volumes of MgO over a wide range of temperature and pressure. In addition, the MD simulation reproduces accurately the measured volume compression data of MgO up to 100GPa at 300K. It is demonstrated that the MD simulated P－V－T equation of state of MgO could be applied as a useful internal pressure calibration standard at elevated temperatures and high pressures.     

X‐ray reflectivity measurements of liquid/solid interfaces under high hydrostatic pressure conditions

A high‐pressure cell for in situ X‐ray reflectivity measurements of liquid/solid interfaces at hydrostatic pressures up to 500 MPa (5 kbar), a pressure regime that is particularly important for the study of protein unfolding, is presented. The original set‐up of this hydrostatic high‐pressure cell is discussed and its unique properties are demonstrated by the investigation of pressure‐induced adsorption of the protein lysozyme onto hydrophobic silicon wafers. The presented results emphasize the enormous potential of X‐ray reflectivity studies under high hydrostatic pressure conditions for the in situ investigation of adsorption phenomena in biological systems.     

Effect of high pressure processing on the preservation of frozen and re-thawed sliced cod (Gadus morhua) and salmon (Salmo salar) fillets

Cod and salmon are both widely found in the seafood market, but those products are easily spoiled. This work reports on the investigation of the effects of three moderate pressure values (150, 300 and 450?MPa) applied for 5?min at 20°C on crude sliced cod and salmon fillets. It was found that high pressure processing (HPP) significantly reduced the microbial load during refrigerated storage for up to 14 days. As expected, the most effective treatment was 450?MPa because it inhibited microbial growth. This process affected the hardness, lightness, lipid oxidation, protein denaturation and oxidation. The fish muscle composition (lipid amount and protein profile) played a main role in the changes promoted by pressure. HPP permits the shelf life of the raw product at 4°C to be increased with minimal changes in the organoleptic characteristics and to enable crude consumption.     

Effect of high pressure on the reaction between bovine myofibrils and cathepsin D

This study deals with the effect of high pressure [50-500 MPa] and time of treatment [20-900 s] on the reaction between myofibrils and cathepsin D from bovine post mortem meat, using Surface Response Methodology. We shown that every high pressure treatment enhanced activity of cathepsin D as evaluated on haemoglobin as a substrate or on control meat myofibrils. We also put in evidence that cathepsin D could carry out the hydrolysis of high pressure treated myofibrils. At last we studied the action of pressurised cathepsin D on pressurised myofibrils, and proved that the hydrolysis was increasing up to 170 MPa and then decreased; above 300 MPa the activity was lower than with control cathepsin D and control myofibrils. Thus above 300 MPa recognition of natural substrate is affected by high pressure induced modifications. These results may help to explain why high pressure treatment of post rigor meat is not able to increase tenderness.     

高压对米曲霉理化性质影响及诱变的研究

 在100~400 MPa压力、保压20 min的条件下处理酱油酿造菌种——米曲霉,研究高压对米曲霉存活率、形态特征、生理性质、蛋白酶、淀粉酶活性等的影响,并诱变筛选优良菌株。结果表明：高压对米曲霉的存活率、形态特征有明显的影响;压力对蛋白酶及淀粉酶活性的影响也有特异的规律,即在一定压力范围内（0.1~200 MPa）蛋白酶的活性随着压力的增加而减小,但随着压力的进一步升高（200~400 MPa）蛋白酶的活性又逐渐增强,在300 MPa时超过对照组,400 MPa时蛋白酶的活性达到最高值;淀粉酶在0.1~100 MPa时活性下降,在200 MPa时其平均的糊化和糖化活性最强、活力最高,当压力升高活性又开始降低,400 MPa时几乎又回到对照值。另外,高压处理后获得一株理想的变异菌株HP300a：生长速度快、孢子数量多、蛋白酶活力高,且不易被杂菌污染。其成曲的几项主要指标均优于对照株,酿出酱油的几项主要指标也明显优于对照株。为利用高压诱变筛选米曲霉优良菌种、提高酿造酱油产品的产量及质量提供了理论依据,并发现了高压处理米曲霉引起其蛋白酶及淀粉酶活性改变的特殊规律。     

Effect of pressure on the thermal expansion of MgO up to 200~GPa

Constant temperature and pressure molecular dynamics (MD) simulations are performed to investigate the thermal expansivity of MgO at high pressure, by using effective pair-wise potentials which consist of Coulomb, dispersion, and repulsion interactions that include polarization effects through the shell model (SM). In order to take into account non-central forces in crystals, the breathing shell model (BSM) is also introduced into the MD simulation. We present a comparison between the volume thermal expansion coefficient α dependences of pressure P at 300 and 2000~K that are obtained from the SM and BSM potentials and those derived from other experimental and theoretical methods in the case of MgO. Compared with the results obtained by using the SM potentials, the MD results obtained by using BSM potentials are more compressible. In an extended pressure and temperature range, the α value is also predicted. The properties of MgO in a pressure range of 0--200~GPa at temperatures up to 3500~K are summarized.     

白蛋白酸致变性的动态激光散斑研究

利用动态激光散斑的方法研究了白蛋白的酸致变性过程。首先,利用动态散斑理论模拟生成了动态散斑序列图;然后,利用模拟和实验散斑图的时间序列散斑图及其灰度共生矩阵对白蛋白的酸致变性过程进行了分析;接着,又利用灰度共生矩阵的惯性矩和不同阶段的四幅散斑图的平均对比度图对该过程进行了更深入的研究。理论模拟和实验研究结果表明,在白蛋白酸致变性过程中,胶体溶液中的蛋白质微粒的运动由剧烈逐渐变得缓慢;同时,微粒数量减少而微粒尺寸增加。研究表明,动态激光散斑方法是一种实时、快速、有效的研究白蛋白变性过程的新手段。     

High Pressure/Thermal Treatments Effects on Functionality of Comminuted Muscle from Different Meat Species

This paper analyses the response of comminuted meat from different species (pork, chicken, turkey and ostrich) to heating (45 and 70 °C/30 min) under pressure (400 MPa) condition. The results (protein solubility, thermal analysis and rheological properties) indicate that the effect of temperature on protein denaturation is reduced if heating takes place at high pressure; then, the pressurization process partially preserves the protein from thermal denaturation. They also show that it is the processing conditions rather than the species that modulate protein thermal stability.