Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran.
Division of Theoretical Chemistry, Lund University, Lund, Sweden.
Phys Chem Chem Phys. 2022 Feb 9;24(6):3647-3654. doi: 10.1039/d1cp05218g.
Computational methods to understand interactions in bio-complex systems are however limited to time-scales typically much shorter than in Nature. For example, on the nanoscale level, interactions between nanoparticles (NPs)/molecules/peptides and membranes are central in complex biomolecular processes such as membrane-coated NPs or cellular uptake. This can be remedied by the application of Jarzynski's equality where thermodynamic properties are extracted from non-equilibrium simulations. Although, the out of equilibrium work leads to non-conservative forces. We here propose a correction Pair Forces method, that removes these forces. Our proposed method is based on the calculation of pulling forces in backward and forward directions for the Jarzynski free-energy estimator using steered molecular dynamics simulation. Our results show that this leads to much improvement for NP-membrane translocation free energies. Although here we have demonstrated the application of the method in molecular dynamics simulation, it could be applied for experimental approaches.
然而，用于理解生物复杂系统相互作用的计算方法的时间尺度通常远远短于自然界。例如，在纳米尺度上，纳米颗粒（NP）/分子/肽与膜之间的相互作用在复杂的生物分子过程中至关重要，例如膜包覆的 NP 或细胞摄取。这可以通过应用 Jarzynski 等式来解决，其中从非平衡模拟中提取热力学性质。然而，非平衡功会导致非保守力。我们在这里提出了一种修正的对力方法，可以消除这些力。我们提出的方法基于使用导向分子动力学模拟，为 Jarzynski 自由能估算器计算向后和向前的拉力。我们的结果表明，这可以大大提高 NP 膜转位自由能的估算精度。尽管我们在这里已经证明了该方法在分子动力学模拟中的应用，但它也可以应用于实验方法。
