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.     

Uncertain and negative evidence in continuous time Bayesian networks

The continuous time Bayesian network (CTBN) enables reasoning about complex systems by representing the system as a factored, finite-state, continuous-time Markov process. Inference over the model incorporates evidence, given as state observations through time. The time dimension introduces several new types of evidence that are not found with static models. In this work, we present a comprehensive look at the types of evidence in CTBNs. Moreover, we define and extend inference to reason under uncertainty in the presence of uncertain evidence, as well as negative evidence, concepts extended to static models but not yet introduced into the CTBN model.     

环形线负载驱动变曲率反射镜技术

从薄板弹性理论出发,对可实现曲率变化的环形线负载驱动模型进行分析,给出了基于该模型的大镜厚比变曲率反射镜的形变方程.以较小的驱动力实现较大的中心形变为目标,利用MATLAB软件对不同反射镜厚度、驱动环半径下的反射镜形变情况进行模拟计算,结果表明,反射镜厚度范围在2~4 mm之间、驱动环半径数值在反射镜有效半径1/2处最佳.以此为依据,设计并研制了口径为100 mm、厚度为3 mm的铍青铜环形线负载驱动变曲率反射镜结构及原型样片,给出了变曲率反射镜整体结构前10阶的振动模态分析结果.完成装配后,反射镜原型样片的面形精度接近λ/30(λ为波长).对该结构进行极限曲率变化和面形精度保持的验证实验,通过对变曲率反射镜结构进行改进,环形线负载驱动能够实现超过30个波长(632.8 nm)的中心形变,且面形精度的变化与反射镜中心矢高的变化呈弱相关.     

用从头算方法研究GeCl2分子的非谐振力场和光谱常数

用从头算方法的MP2和CCSD（T）方法结合cc-pVTZ基组计算了二氯化锗同位素（⁷⁰GeCl₂、⁷²GeCl₂和⁷⁶GeCl₂）分子的平衡结构、光谱常数和非谐振力场.二氯化锗的几何结构、转动常数、振转相互作用常数、谐频、非谐振常数、四次和六次离心畸变常数、三次和四次力常数的计算结果与实验结果符合较好,二氯化锗分子的同位素效应较小,可能的原因是Ge同位素的质量变化相对较小.两种方法计算的结果均与实验结果符合,但CCSD（T）方法比MP2计算结果的偏差稍大一些,可能的原因是CCSD（T）方法在描述过共价Cl原子的电子相关时不够充分.     

抗生物素蛋白与DNA相互作用的单分子研究

抗生物素蛋白(avidin)在生物单分子实验中被广泛用于DNA与修饰表面的连接,同时avidin也可作为一种DNA载体用于基因治疗中.本文利用原子力显微镜(AFM)、动态光散射(DLS)、单分子磁镊(MT)技术系统地研究了avidin与DNA之间的相互作用,以及avidin引起DNA凝聚的机理.首先通过AFM对avidin-DNA复合体形貌进行观察,发现不但有avidin导致DNA凝聚的环状形貌,同时也存在avidin自身聚集引起的DNA凝聚现象,通过定量分析,发现其凝聚尺寸越来越小,而当avidin浓度大于2 ng·μL~(-1)时,其凝聚尺寸又突然变大.DLS实验结果也显示了同样的规律,伴随着avidin浓度的升高,DNA的粒径大小从大约170 nm减小到125 nm左右,其电泳迁移率由-2.76(10~(-4)cm~2·V~(-1)·s~(-1))变化到-0.1(10~(-4)cm~2·V~(-1)·~(-1)).此外,通过MT技术的力谱曲线变化,发现avidin导致的DNA凝聚与其他多价离子相比,长度的变化曲线几乎呈线性变化,偶尔存在少而小的阶跃,这种变化趋势与组蛋白的变化曲线更相似.因此可以判断,avidin导致DNA凝聚是由avidin与DNA的静电吸引和avidin自身聚集两种相互作用引起的.     

用水物理模型表征纯水离子积

纯水被描述为离解成水合氢离子(H₃O)¹⁺和氢氧根离子(HO)^1-, 平衡常数在液态水的温度和压力范围内被称为离子积,即两种离子的平衡态浓度的乘积. 用非线性最小二乘法把实验数据拟合成基于化学热力学的平衡态方程. 本工作提出一个全新的、基于统计物理的水离子积方程,其中的离子为带正电的质子和带负电的质子空穴(质穴). 把0-100 ℃纯水的实验数据用非线性最小二乘法拟合的方程,给出的结果比35年工业标准更准确.     

The secondary Bjerknes force between two gas bubbles under dual-frequency acoustic excitation

The secondary Bjerknes force is one of the essential mechanisms of mutual interactions between bubbles oscillating in a sound field. The dual-frequency acoustic excitation has been applied in several fields such as sonochemistry, biomedicine and material engineering. In this paper, the secondary Bjerknes force under dual-frequency excitation is investigated both analytically and numerically within a large parameter zone. The unique characteristics (i.e., the complicated patterns of the parameter zone for sign change and the combination resonances) of the secondary Bjerknes force under dual-frequency excitation are revealed. Moreover, the influence of several parameters (e.g., the pressure amplitude, the bubble distance and the phase difference between sound waves) on the secondary Bjerknes force is also investigated numerically.     

Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field

Current all-atom force fields often fail to recognize the native structure of a protein as the lowest free energy minimum. One possible cause could be the mathematical form of the potential based on the assumption that the conformation of a residue is independent of its neighbors. Here, using quantum mechanical (QM) methods (MP2/6-31g**//HF/6-31g** and MP2/cc-pVDZ//cc-pVDZ//HF/cc-pVDZ), the intrinsic correctness of the gas phase terms (without solvation) of the Amber ff03 and ff99 potentials are examined by testing their ability to reproduce the relative 3(10)-helix versus extended structure stabilities in the gas phase for 1-7-residue alanine, valine, leucine, and isoleucine homopolypeptides. The 3(10)-helix versus extended state stability strongly depends on chain length and less on the amino acid identity. The helical conformation becomes lower in energy than the extended conformation for all tested peptides longer than two residues, and its stability increases with the increase of chain length. The ff03 potential better describes the 3(10)-helix versus extended state energy than ff99 and also reproduces the curvature of the relative helix-extended state energies. Therefore, the mathematical form of the Amber potential is sufficient to describe the local effect of 3(10)-helix versus extended structure stabilization in the gas phase. However, the energy curves are shifted and the backbone geometries differ compared with the QM results. This may cause significant geometric discrepancies between native and predicted structures. Therefore, extant molecular mechanics force fields, such as Amber, need refinement of their parameters to correctly describe helix-extended state energetics and geometry of major conformations.     

Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united-atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all-atom implicit solvation method (C22 with GBMV), and an all-atom explicit solvation method (C22 with TIP3P). The adsorption behavior of each peptide was characterized by the calculation of the potential of mean force as a function of peptide-surface separation distance. The results from the C22/TIP3P model suggest that hydrophobic peptides exhibit relatively strong adsorption behavior, polar and positively-charged peptides exhibit negligible to relatively weak favorable interactions with the surface, and negatively-charged peptides strongly resist adsorption. Compared to the TIP3P model, the ACE and GBMV implicit solvent models predict much stronger attractions for the hydrophobic peptides as well as stronger repulsions for the negatively-charged peptides on the CH(3)-SAM surface. These comparisons provide a basis from which each of these implicit solvation methods may be reparameterized to provide closer agreement with explicitly represented solvation in simulations of peptide and protein adsorption to functionalized surfaces.