CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry
CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry
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CoSIMS：用于离子淌度谱分析的基于优化轨迹的碰撞模拟器
DOI：
10.1021/acs.jpcb.9b01018
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Chen, Alan A.
中科院分区：
文献类型：
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作者：
Myers, Christopher A.;D’Esposito, Rebecca J.;Fabris, Daniele;Ranganathan, Srivathsan V.;Chen, Alan A.
一个新的，多线程，基于轨迹方法的软件平台，CoSIMS，揭示和比较参考MOBCAL碰撞截面（CCS）。CoSIMS采用各种分子力学算法来减少模拟数千次缓冲气体-离子碰撞所需的计算资源，包括忽略长距离的伦敦色散相互作用，以及通过椭球投影近似去除对总CCS贡献不大的轨迹。所展示的程序用于计算碳富勒烯，蛋白质和DNA链的碰撞截面的各种长度，大小和分子量，并将这些与由MOBCAL计算的CCS进行比较。通过这种分析，它表明，上述算法的应用程序，使更快，更合理的CCS计算比MOBCAL高度细长的分子，如核酸;对于所有其他分子，CoSIMS是能够复制的CCS产生的MOBCAL的轨迹方法在百分之几。总的来说，CoSIMS能够计算几乎相同的CCS作为MOBCAL在近2个数量级的CPU时间，由于各种数值方法实施到软件中，即使在一个单一的CPU核心上运行。
A new, multithreaded, trajectory method based software platform, CoSIMS, is revealed and compared to reference MOBCAL collision cross sections (CCS). CoSIMS employs various molecular mechanics algorithms to lessen the computational resources required to simulate thousands of buffer gas–ion collisions, including the neglect of London dispersion interactions at long distances and the removal of trajectories that insignificantly contribute to the total CCS via an ellipsoidal projection approximation. The showcased program is used to calculate the collision cross sections of carbon fullerenes, proteins, and DNA strands of various lengths, sizes, and molecular weights, and these are compared against the CCSs calculated by MOBCAL. Through this analysis, it is shown that the application of the aforementioned algorithms enables both faster and more reasonable CCS calculations than MOBCAL for highly elongated molecules such as nucleic acids; for all other molecules, CoSIMS is able to reproduce the CCSs generated by MOBCAL’s trajectory method within a few percent. Overall, CoSIMS is able to calculate nearly identical CCSs as MOBCAL in nearly 2 orders of magnitude less CPU time due to the various numerical methods implemented into the software, even when run on a single CPU core.