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Myers CA, D'Esposito RJ, Fabris D, et al. CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry. J Phys Chem B. 2019;123(20):4347-4357doi: 10.1021/acs.jpcb.9b01018.
Myers, C. A., D'Esposito, R. J., Fabris, D., Ranganathan, S. V., & Chen, A. A. (2019). CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry. The journal of physical chemistry. B, 123(20), 4347-4357. https://doi.org/10.1021/acs.jpcb.9b01018
Myers, Christopher A, et al. "CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry." The journal of physical chemistry. B vol. 123,20 (2019): 4347-4357. doi: https://doi.org/10.1021/acs.jpcb.9b01018
Myers CA, D'Esposito RJ, Fabris D, Ranganathan SV, Chen AA. CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry. J Phys Chem B. 2019 May 23;123(20):4347-4357. doi: 10.1021/acs.jpcb.9b01018. Epub 2019 May 10. PMID: 31042389; PMCID: PMC6958516.
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J Phys Chem B. 2019 May 23;123(20):4347-4357. doi: 10.1021/acs.jpcb.9b01018. Epub 2019 May 10.

CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry.

The journal of physical chemistry. B

Christopher A Myers, Rebecca J D'Esposito, Daniele Fabris, Srivathsan V Ranganathan, Alan A Chen

Affiliations

  1. Department of Physics , University at Albany (SUNY) , Albany , New York 12222 , United States.
  2. Department of Chemistry , University at Albany (SUNY) , Albany , New York 12222 , United States.
  3. The RNA Institute , University at Albany (SUNY) , Albany , New York 12222 , United States.
  4. Department of Biological Sciences , University at Albany (SUNY) , Albany , New York 12222 , United States.

PMID: 31042389 PMCID: PMC6958516 DOI: 10.1021/acs.jpcb.9b01018

Abstract

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.

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