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Coarse-grained models have proven helpful for simulating complex systems over long timescales to provide molecular insights into various processes.
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de Pablo, J. J. Coarse-Grained Simulations of Macromolecules: From DNA to Nanocomposites. Annual Review of Physical Chemistry 2011
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Clark, A. J.; McCarty, J.; Lyubimov, I. Y.; Guenza, M. G. Thermodynamic Consistency in Variable-Level Coarse Graining of Polymeric Liquids. Physical Review Letters 2012
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Gkeka, P. et al. Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems. Journal of Chemical Theory and Computation 2020
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Gao, R.; Nijkamp, E.; Kingma, D. P.; Xu, Z.; Dai, A. M.; Wu, Y. N. Flow contrastive estimation of energy-based models. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. 2020; pp 7518–7528
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Ding, X.; Zhang, B. Computing Absolute Free Energy with Deep Generative Models. Journal of Physical Chemistry B 2020
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Souza, P. C. T. et al. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nature Methods 2021
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Joseph, J. A.; Reinhardt, A.; Aguirre, A.; Chew, P. Y.; Russell, K. O.; Espinosa, J. R.; Garaizar, A.; Collepardo-Guevara, R. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. Nature Computational Science 2021
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Farr, S. E.; Woods, E. J.; Joseph, J. A.; Garaizar, A.; Collepardo-Guevara, R. Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions. Nature Communications 2021
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Latham, A. P.; Zhang, B. Consistent Force Field Captures Homologue-Resolved HP1 Phase Separation. J. Chem. Theory Comput. 2021
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Ding, X.; Zhang, B. DeepBAR: A Fast and Exact Method for Binding Free Energy Computation. Journal of Physical Chemistry Letters 2021
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Latham, A. P.; Zhang, B. Unifying coarse-grained force fields for folded and disordered proteins. Current Opinion in Structural Biology 2022
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