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Publications

Research Gate Profile

Recent Publications:

E. R. Beyerle, M. G. Guenza “Comparison between slow anisotropic LE4PD fluctuations and the principal component analysis mode of ubiquitin” J. Chem. Phys. 154, 12411(1-21) (2021) DOI: 10.1063/5.0041211 

E. R. Beyerle, M. Dinpajooh, H. Ji, P. H. von Hippel, A. H. Marcus, and M. G. Guenza “Dinucleotides as simple models of the base stacking-unstacking component of DNA ‘breathing’ mechanisms” Nucleic Acid Research, 49(4), 1872-1885 (2021). PMCID: PMC7913701. DOI: 10.1093/nar/gkab015. 

E. R. Beyerle, M. G. Guenza "Kinetics analysis of ubiquitin local fluctuations with Markov state modeling of the LE4PD normal modes” J. Chem. Phys. 151, 164119(1-13) (2019) DOI: 10.1063/1.5123513

M. Dinpajooh, M. G. Guenza “Can pure polymer liquids be represented at two different resolutions simultaneously?" J. Chem. Phys., 151, 061102-(1-5) (2019). DOI: 10.1063/1.5115791. 

M. G. Guenza, M. Dinpajooh, J. McCarty, I. Y. Lyubimov “Accuracy, Transferability, and Efficiency of Coarse-Grained Models of Molecular Liquids” The Journal of Physical Chemistry B, 122(45), 10257-10278 (2018). DOI: 10.1021/acs.jpcb.8b06687. Publication Selected as Editor’s Pick and Feature Article.

M. Dinpajooh, M. G. Guenza “Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency” Soft Matter, 14, 7126-7144 (2018). Cover paper.

M. Dinpajooh, and M. G. Guenza “On the Density Dependence of the Integral Equation Coarse-Graining Effective Potential" The Journal of Physical Chemistry B, 122(13), 3426-3440 (2018). DOI:10.1021/acs.jpcb.7b10494.

P. G. Romano and M. G. Guenza “GRadient Adaptive Decomposition (GRAD) Method: Optimized Refinement Along Macrostate Borders in Markov State Models" The Journal of Chemical Infromation and Modeling 57, 2729-2740 (2017). 

J. Copperman, M. Dinpajooh, E. Beyerle, and M. G. Guenza “Universality and specificity in protein fluctuation dynamics" Physical Review Letters, 119, 158101 (2017).

M. Dinpajooh, and M. G. Guenza “Thermodynamic Consistency in the Structure-based Integral Equation Coarse-Grained Method" Polymers, 117, 282-286 (2017).

E. deLorimier, M. N. Hinman, J. Copperman, K. Datta, M. Guenza, and J. A. Berglund “Pseudouridine Modification Inhibits Muscleblind-like 1(MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility” Journal of Biological Chemistry, 292, 4350-4357 (2017).

M. G. Guenza "Thermodynamically Consistent Coarse-Graining of Polymers" in "Coarse-Grained Modeling of Biomolecules" (Series in Computational Biophysics by Tylor & Francis Publisher, G. Papoian Ed. 2017) arXiv:1509.08546.