Principal Publications

Cummings, P. T.; McCabe, C.; Iacovella, C. R.; Ledeczi, A.; Jankowski, E.; Jayaraman, A.; Palmer, J. C.; Maginn, E. J.; Glotzer, S. C.; Anderson, J. A.; Siepmann, J. I.; Potoff, J.; Matsumoto, R. A.; Gilmer, J. B.; DeFever, R. S.; Singh, R.; Crawford, B. Open-Source Molecular Modeling Software in Chemical Engineering Focusing on the Molecular Simulation Design Framework. AIChE Journal 2021, 67 (3), e17206. downloadris downloadbib

Thompson, M. W.; Gilmer, J. B.; Matsumoto, R. A.; Quach, C. D.; Shamaprasad, P.; Yang, A. H.; Iacovella, C. R.; McCabe, C.; Cummings, P. T. Towards Molecular Simulations That Are Transparent, Reproducible, Usable by Others, and Extensible (TRUE). Molecular Physics 2020, 118 (9–10), e1742938. downloadris downloadbib

Klein, C.; Summers, A. Z.; Thompson, M. W.; Gilmer, J. B.; McCabe, C.; Cummings, P. T.; Sallai, J.; Iacovella, C. R. Formalizing Atom-Typing and the Dissemination of Force Fields with Foyer. Computational Materials Science 2019, 167, 215–227. downloadris downloadbib

Klein, C.; Sallai, J.; Jones, T. J.; Iacovella, C. R.; McCabe, C.; Cummings, P. T. A Hierarchical, Component Based Approach to Screening Properties of Soft Matter. In Foundations of Molecular Modeling and Simulation: Select Papers from FOMMS 2015; Snurr, R. Q., Adjiman, C. S., Kofke, D. A., Eds.; Molecular Modeling and Simulation; Springer Singapore: Singapore, 2016; pp 79–92. downloadris downloadbib

Publications around the MoSDeF Ecosystem

Craven, N. C.; Gilmer, J. B.; Spindel, C. J.; Summers, A. Z.; Iacovella, C. R.; McCabe, C. Examining the Self-Assembly of Patchy Alkane-Grafted Silica Nanoparticles Using Molecular Simulation. J. Chem. Phys. 2021, 154 (3), 034903.

DeFever, R. S.; Matsumoto, R. A.; Dowling, A. W.; Cummings, P. T.; Maginn, E. J. MoSDeF Cassandra: A Complete Python Interface for the Cassandra Monte Carlo Software. Journal of Computational Chemistry 2021 (n/a).

Summers, A. Z.; Gilmer, J. B.; Iacovella, C. R.; Cummings, P. T.; McCabe, C. MoSDeF, a Python Framework Enabling Large-Scale Computational Screening of Soft Matter: Application to Chemistry-Property Relationships in Lubricating Monolayer Films. J. Chem. Theory Comput. 2020, 16 (3), 1779–1793.

Henry, M. M.; Thomas, S.; Alberts, M.; Estridge, C. E.; Farmer, B.; McNair, O.; Jankowski, E. General-Purpose Coarse-Grained Toughened Thermoset Model for 44DDS/DGEBA/PES. Polymers 2020, 12 (11), 2547.

Jankowski, E.; Ellyson, N.; Fothergill, J. W.; Henry, M. M.; Leibowitz, M. H.; Miller, E. D.; Alberts, M.; Chesser, S.; Guevara, J. D.; Jones, C. D.; Klopfenstein, M.; Noneman, K. K.; Singleton, R.; Uriarte-Mendoza, R. A.; Thomas, S.; Estridge, C. E.; Jones, M. L. Perspective on Coarse-Graining, Cognitive Load, and Materials Simulation. Computational Materials Science 2020, 171, 109129.

Ramasubramani, V.; Dice, B. D.; Harper, E. S.; Spellings, M. P.; Anderson, J. A.; Glotzer, S. C. Freud: A Software Suite for High Throughput Analysis of Particle Simulation Data. Computer Physics Communications 2020, 254, 107275.

Butler, B. L.; Ramasubramani, V.; Anderson, J. A.; Glotzer, S. C. HOOMD-Blue Version 3.0 A Modern, Extensible, Flexible, Object-Oriented API for Molecular Simulations. Proceedings of the 19th Python in Science Conference 2020, 24–31.

Kapoor, U.; Kulshreshtha, A.; Jayaraman, A. Development of Coarse-Grained Models for Poly(4-Vinylphenol) and Poly(2-Vinylpyridine): Polymer Chemistries with Hydrogen Bonding. Polymers 2020, 12 (11), 2764.

Dice, B. D.; Ramasubramani, V.; Harper, E. S.; Spellings, M. P.; Anderson, J. A.; Glotzer, S. C. Analyzing Particle Systems for Machine Learning and Data Visualization with Freud. Proceedings of the 18th Python in Science Conference 2019, 27–33.

Matsumoto, R.; Thompson, M. W.; Cummings, P. T. Ion Pairing Controls Physical Properties of Ionic Liquid-Solvent Mixtures. J. Phys. Chem. B 2019, 123 (46), 9944–9955.

Cummings, P. T.; Gilmer, J. B. Open-Source Molecular Modeling Software in Chemical Engineering. Current Opinion in Chemical Engineering 2019, 23, 99–105.

Thompson, M. W.; Matsumoto, R.; Sacci, R. L.; Sanders, N. C.; Cummings, P. T. Scalable Screening of Soft Matter: A Case Study of Mixtures of Ionic Liquids and Organic Solvents. J. Phys. Chem. B 2019, 123 (6), 1340–1347.

Kulshreshtha, A.; Modica, K. J.; Jayaraman, A. Impact of Hydrogen Bonding Interactions on Graft–Matrix Wetting and Structure in Polymer Nanocomposites. Macromolecules 2019, 52 (7), 2725–2735.