Abstract Amphiphile-based aggregates are extensively used in numerous applications for encapsulation, storage, transport and delivery of toxic, active molecules due to the structural properties of the aggregates. The properties of the aggregates in turn are dictated by the molecular architecture of the amphiphiles. A complete understanding of the multiscale architecture–structure–function relationship for amphiphile-based aggregates requires the simultaneous resolution of the self-assembly of amphiphilic molecules along with an understanding of the role of various long range physical interactions including hydrodynamics. A multiscale computational approach such as the hybrid Molecular Dynamics–Lattice Boltzmann technique is able to fulfill most of those requirements. However, existing implementations only account for static coupling between the Molecular Dynamics technique and the Lattice Boltzmann method, and hence are unable to resolve the changes in the solvent-amphiphile interface during processes such as self-assembly and interfacial adsorption. In this study, a new implementation incorporating a dynamic coupling scheme between the Molecular Dynamics technique and the Lattice Boltzmann method is introduced so as to resolve dynamical changes in interfaces. The application of the new implementation to the self-assembly of phospholipids yields results which are in good agreement with computation, experiments and theory. In particular, we found the scaling exponent α of the cluster number (N(t) = C t α ) to be ∼ 1. Program summary Program Title: fix_lb_fluid_dynamic_coupling.cpp, fix_lb_fluid_dynamic_coupling.h Program Files doi: http://dx.doi.org/10.17632/wr4mgv35j5.1 Licensing provisions: GNU General Public License 3 Programming language: C++ Journal Reference of previous version: Mackay, F. E., Ollila, S. T., & Denniston, C. (2013). Hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid. Computer Physics Communications, 184(8), 2021-2031. Does the new version supersede the previous version? No. Reasons for new version: Enable dynamic coupling between Molecular Dynamics and Lattice Boltzmann. Summary of revisions: Determination of whether the number of neighbors for each Molecular Dynamics bead is above a predetermined threshold set by the user. If the number of neighbors is above the threshold, the Molecular Dynamics bead is decoupled from the Lattice Boltzmann grid. Nature of problem: Determination of the criteria and method for decoupling Molecular Dynamics beads from the Lattice Boltzmann grid. Solution method: The number of neighbors for each Molecular Dynamics bead which lie within the interaction potential cutoff distance is determined. If the number of neighbors is above a critical threshold, the reference Molecular Dynamics bead is decoupled from the Lattice Boltzmann grid.

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混合分子动力学-格子玻尔兹曼方法中动态耦合的实现：两亲物的建模聚合

摘要 基于两亲物的聚集体由于聚集体的结构特性而广泛用于封装、储存、运输和递送有毒活性分子的许多应用。聚集体的性质又由两亲物的分子结构决定。对基于两亲物质的聚集体的多尺度结构-结构-功能关系的完整理解需要同时解决两亲分子的自组装以及对包括流体动力学在内的各种长程物理相互作用的作用的理解。多尺度计算方法（例如混合分子动力学-格子玻尔兹曼技术）能够满足大多数这些要求。然而，现有的实现只考虑了分子动力学技术和格子玻尔兹曼方法之间的静态耦合，因此无法解决自组装和界面吸附等过程中溶剂-两亲界面的变化。在这项研究中，引入了一种结合分子动力学技术和格子玻尔兹曼方法之间的动态耦合方案的新实现，以解决界面的动态变化。将新实现应用于磷脂自组装产生的结果与计算、实验和理论非常吻合。特别地，我们发现簇数的标度指数 α (N(t) = C t α ) 为∼1。 程序摘要 Program Title: fix_lb_fluid_dynamic_coupling.cpp, fix_lb_fluid_dynamic_coupling。h 程序文件 doi：http://dx.doi.org/10.17632/wr4mgv35j5.1 许可条款：GNU 通用公共许可证 3 编程语言：C++ 期刊 先前版本参考：Mackay, FE, Ollila, ST, & Denniston, C . (2013)。通过晶格-玻尔兹曼流体在 LAMMPS 中实现的水动力。计算机物理通信，184(8)，2021-2031。新版本会取代旧版本吗？否。新版本的原因：启用分子动力学和格子玻尔兹曼之间的动态耦合。修订摘要：确定每个分子动力学珠子的邻居数量是否高于用户设置的预定阈值。如果邻居数高于阈值，则分子动力学珠子与格子玻尔兹曼网格解耦。问题性质：确定从格子 Boltzmann 网格中解耦分子动力学珠子的标准和方法。求解方法：确定位于相互作用电位截止距离内的每个分子动力学珠的邻居数。如果邻居数高于临界阈值，则参考分子动力学珠子与格子玻尔兹曼网格解耦。