Alternative routes to equivalent classical models of a quantum system

<正>Coarse-graining of some sort is a fundamental and unavoidable step in any attempt to derive the classical mechanical behavior from the quantum formalism.We utilize the two-mode Bose-Hubbard model to illustrate how different coarse-grained systems can be naturally associated with a fixed quantum system if it is compatible with different dynamical algebras.Alternative coarse-grained systems generate different evolutions of the same physical quantities,and the difference becomes negligible only in the appropriate macro-limit.     

某矿山金矿石样品加工及分析方法优化研究

某矿山金矿石样品中存在中粗颗粒金,颗粒金的存在将对分析样品的均匀性和代表性产生影响。通过棒磨、密封粉碎及盘磨等方式研究,选择出最优的样品加工方式,同时通过分析方法比对,选择出最优的样品分析方法。实验确定金矿石采用圆盘细碎机加工至样品粒度不大于0.074 mm,混匀后即获得分析试样。分析试样经王水消解后采用泡沫吸附进行富集,火焰原子吸收光谱法测定。通过研究,取得最优的金矿样品加工和分析方案,为某矿山提供了高品质的金储量评估数据。     

磷脂微滴囊泡化的介观模拟

发展了一种非显示溶剂的粗粒化三粒子磷脂模型,该模型明确反映磷脂分子的双尾结构．模型分别采用变形的MIE作用势和Harmonic作用势描述分子间非成键和分子内成键相互作用,粗粒化力场参数通过拟合DPPC双分子层的结构和力学性质获得．该粗粒化模型成功重现了磷脂分子从随机初始态到双分子层和从盘状结构到囊泡的形成过程．应用该模型系统研究了球形和柱形磷脂微滴囊泡化的过程,结果表明此模型能有效地模拟介观尺度下复杂磷脂囊泡的形成及演化．     

Comparative molecular dynamics and Monte Carlo study of statistical properties for coarse-grained heteropolymers

Employing a simple hydrophobic-polar heteropolymer model, we compare thermodynamic quantities obtained from Andersen and Nosé-Hoover molecular dynamics as well as replica-exchange Monte Carlo methods. We find qualitative correspondence in the results, but serious quantitative differences using the Nosé-Hoover chain thermostat. For analyzing the deviations, we study different parameterizations of the Nosé-Hoover chain thermostat. Autocorrelations from molecular dynamics and Metropolis Monte Carlo runs are also investigated.     

Group-valued measures on coarse-grained quantum logics

In [3] it was shown that a (real) signed measure on a cyclic coarse-grained quantum logic can be extended, as a signed measure, over the entire power algebra. Later ([9]) this result was re-proved (and further improved on) and, moreover, the non-negative measures were shown to allow for extensions as non-negative measures. In both cases the proof technique used was the technique of linear algebra. In this paper we further generalize the results cited by extending group-valued measures on cyclic coarse-grained quantum logics (or non-negative group-valued measures for lattice-ordered groups). Obviously, the proof technique is entirely different from that of the preceding papers. In addition, we provide a new combinatorial argument for describing all atoms of cyclic coarse-grained quantum logics.     

Martini coarse-grained model for polyethylenimine

As a polycation with diverse applications in biomedical and environmental engineering, polyethylenimine (PEI) can be synthesized with varying degrees of branching, polymerization, and can exist in different protonation states. There have been some interests in molecular modeling of PEI at all-atom or coarse-grained (CG) levels, but present CG models are limited to linear PEIs. Here we present the methodology to systematically categorize bond lengths, bond angles and dihedral angles, which allows us to model branched PEIs. The CG model was developed under the Martini scheme based on eight ~600 Da PEIs, with four different degree of branching at two different protonation states. Comparison of the CG model with all-atom simulations shows good agreement for both local (distributions for bonded interactions) and global (end-to-end distance, radius of gyration) properties, with and without salt. Compatibility of the PEI model with other CG bio-molecules developed under the Martini scheme will allow for large-scale simulations of many PEI-enabled processes. © 2018 Wiley Periodicals, Inc.     

Reaction rate theory for supramolecular kinetics: application to protein aggregation

ABSTRACT

Probing reaction mechanisms of supramolecular processes in soft and biological matter, such as protein aggregation, is inherently challenging. This is because these processes involve multiple molecular mechanisms that are associated with the rearrangement of large numbers of weak bonds, resulting in complex free energy landscapes with many kinetic barriers. Reaction rate measurements at different temperatures can offer unprecedented insights into the underlying molecular mechanisms. However, to be able to interpret such measurements, a key challenge is to establish which properties of the complex free energy landscapes are probed by the reaction rate. Here, we present a reaction rate theory for supramolecular kinetics based on Kramers theory of diffusive reactions over multiple kinetic barriers. We find that reaction rates for protein aggregation are of the Arrhenius–Eyring type and that the associated activation energies probe only one relevant barrier along the respective free energy landscapes. We apply this advancement to interpret, in experiments and in coarse-grained computer simulations, reaction rates of amyloid aggregation in terms of molecular mechanisms and associated thermodynamic signatures. These results suggest a practical extension of the concept of rate-determining steps for complex supramolecular processes and establish a general platform for probing the underlying energy landscape using kinetic measurements.