复杂体系的计算机模拟
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摘要
1.我们使用了动态密度泛函理论对三杂臂星型共聚物以及线性均聚物的共混体系进行了研究。模拟结果表明,有可能仅仅通过线性均聚物的添加就使同一个三杂臂星型共聚物自组装体系的微相结构由一个规整形态变为完全不同的另一个规整形态。这为我们设计并制造不同形态的纳米材料指出了一条新路。
2.我们通过在三杂臂星型共聚物体系中添加线性均聚物的方法尝试对其平衡状态下微相结构的相区尺径进行控制,发现相对而言分散相区的尺径对组分变化敏感,而分散相区间隔的变化则相对较弱;另外添加量超过一定比例时情况也会变的更加复杂。
3.我们构建了大肠杆菌热休克反应的Petri网络模型,并应用化学反应动力学随机算法进行了模拟计算,观察其动力学过程,通过观测体系中平衡态下分子数目与反应速率常数间关系,总结了反应对体系平衡的影响规律,并由观测到的现象,对调控因子α的自身表达的调控机制作出推测:调控因子α的调控机制有可能是受网络控制的。
4.我们使用复制品交换多正则方法在三维非格子模型中模拟了蛋白质链的折叠过程,最终得到了它的天然结构。进一步通过对其各热力学参数的研究,我们讨论了该蛋白质链的折叠行为,认为这是一个遵循成核-凝聚-生长模型(Nuclear-Condensation-GrowthModel)的折叠过程:由最稳定的结构先形成折叠的核,再由这些先形成的核催化蛋白质分子的进一步折叠;并发现这应该是一个存在折叠中间体的两步折叠过程。
1.Ordered microstructures assembled from the mixture of the ABC 3-miktoarm star terpolymers and the linear homopolymers have been investigated by using dynamic density functional theory.The simulations reveal that completely different ordered microphase pattern is found with addition of a few percent homopolymers that is identical in component to one of the arms on the ABC 3-miktoarm star terpolymer.For example,the original density pattern of ABC 3-miktoarm star terpolymers with parameters of N_A=N_B=N_C=10 and X_(AB)=0.90,X_(BC)=X_(CA)=0.45 is in a perfectly ordered knitting feature.However,with gradual addition of the linear polymer same as block C on ABC 3-miktoarm star terpolymer into the system,the density patterns evolve with the volume fraction of the linear polymer from the ordered knitting patterns into the hexagonal patterns.Furthermore,with addition of linear polymers same as block A, lamellar microstructure has finally resulted.The simulation points out a way for designing and manufacturing nanomaterials with totally different microstructures.
2.The linear homopolymers have been added into a ABC 3-miktoarm star terpolymers system by dynamic density functional theory simulation. The areas of B phase domain and the interval between two nearest neighbour B phase domains shift with the accession of the linear polymer.
3.A Petri net model was built to simulate the heat shock response in E.coli.We found several rules in this network by analyzing the simulation results.And we consider the regulation on gene expression ofσ~(32)should be relevant to network control mechanism.
4.The folding process of Honeycutt-Thirumalai model protein chain was simulated with Replica-Exchange Multicanonical Monte Carlo method in a three- dimensional off-lattice model.The results demonstrate that was a two-step folding process according to the Nuclear-Condensation-Growth Model,and the possible conformations of intermediates should include threeβ-sheet segments.The good agreement between the native conformations in simulation and in literature prove the efficiency of our method.
2.我们通过在三杂臂星型共聚物体系中添加线性均聚物的方法尝试对其平衡状态下微相结构的相区尺径进行控制,发现相对而言分散相区的尺径对组分变化敏感,而分散相区间隔的变化则相对较弱;另外添加量超过一定比例时情况也会变的更加复杂。
3.我们构建了大肠杆菌热休克反应的Petri网络模型,并应用化学反应动力学随机算法进行了模拟计算,观察其动力学过程,通过观测体系中平衡态下分子数目与反应速率常数间关系,总结了反应对体系平衡的影响规律,并由观测到的现象,对调控因子α的自身表达的调控机制作出推测:调控因子α的调控机制有可能是受网络控制的。
4.我们使用复制品交换多正则方法在三维非格子模型中模拟了蛋白质链的折叠过程,最终得到了它的天然结构。进一步通过对其各热力学参数的研究,我们讨论了该蛋白质链的折叠行为,认为这是一个遵循成核-凝聚-生长模型(Nuclear-Condensation-GrowthModel)的折叠过程:由最稳定的结构先形成折叠的核,再由这些先形成的核催化蛋白质分子的进一步折叠;并发现这应该是一个存在折叠中间体的两步折叠过程。
1.Ordered microstructures assembled from the mixture of the ABC 3-miktoarm star terpolymers and the linear homopolymers have been investigated by using dynamic density functional theory.The simulations reveal that completely different ordered microphase pattern is found with addition of a few percent homopolymers that is identical in component to one of the arms on the ABC 3-miktoarm star terpolymer.For example,the original density pattern of ABC 3-miktoarm star terpolymers with parameters of N_A=N_B=N_C=10 and X_(AB)=0.90,X_(BC)=X_(CA)=0.45 is in a perfectly ordered knitting feature.However,with gradual addition of the linear polymer same as block C on ABC 3-miktoarm star terpolymer into the system,the density patterns evolve with the volume fraction of the linear polymer from the ordered knitting patterns into the hexagonal patterns.Furthermore,with addition of linear polymers same as block A, lamellar microstructure has finally resulted.The simulation points out a way for designing and manufacturing nanomaterials with totally different microstructures.
2.The linear homopolymers have been added into a ABC 3-miktoarm star terpolymers system by dynamic density functional theory simulation. The areas of B phase domain and the interval between two nearest neighbour B phase domains shift with the accession of the linear polymer.
3.A Petri net model was built to simulate the heat shock response in E.coli.We found several rules in this network by analyzing the simulation results.And we consider the regulation on gene expression ofσ~(32)should be relevant to network control mechanism.
4.The folding process of Honeycutt-Thirumalai model protein chain was simulated with Replica-Exchange Multicanonical Monte Carlo method in a three- dimensional off-lattice model.The results demonstrate that was a two-step folding process according to the Nuclear-Condensation-Growth Model,and the possible conformations of intermediates should include threeβ-sheet segments.The good agreement between the native conformations in simulation and in literature prove the efficiency of our method.
引文
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