The Guenza Lab

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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” Journal of Chemical Information and Modeling 57, 2729-2740 (2017). DOI: 10.1021/acs.jcim.7b00261.

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.

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, 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).

J. Copperman and M. G. Guenza “Mode Localization in the Cooperative Dynamics of Protein Recognition” The Journal of Chemical Physics 145, 015101 (2016).

D. Ozog, A. D. Malony, M. G. Guenza “The UA ↔ CG Workflow: High Performance Molecular Dynamics of Coarse-Grained Polymers” paper to the 24th Euromicro International Conference on Parallel, Distributed and Network-Based Processing – DPD’2016.

J. Copperman and M. G. Guenza “Predicting protein dynamics from structural ensembles” Journal of Chemical Physics, Invited Contribution for Special Topics Issue on Coarse Graining of Macromolecules, Biopolymers, and Membranes” 143, 243131-12 (2015) doi: 10.1063/1.4935575.

A. J. Clark, J. McCarty, and M. G. Guenza “Comment on Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study” 143, 067101 (2015).

M. G. Guenza “Advancements in multi scale modeling: Adaptive resolution simulations and related issues” European Physics Journal Special Topics (EPJ-ST) 224, 2491 (2015).

M. G. Guenza “Thermodynamic consistency and other challenges in coarse-graining models” European Physics Journal Special Topics (EPJ-ST) in “Scale Bridging Techniques in Molecular Simulation: A critical Appraisal” L. Delle Site and C. Hartmann Ed. (2015). DOI: 10.1140/epjst/e2015-02407-x.

D. Ozog, J. McCarty, G. Grossett, A. D. Malony, M. G. Guenza “Fast equilibration of coarse-grained polymeric liquids” Journal of Computational Science 9, 33 (2015).

M. G. Guenza “Structural and thermodynamic consistency in coarse-grained models of macromolecules”  Journal of Physics: Conference Series 640,  0120091 (2015)

J. Copperman, M. G. Guenza “A Coarse-Grained Langevin Equation for Protein Dynamics: Global anisotropy and a mode approach to local complexity” J. Phys. Chem. B, Festschrift issue honoring Branka Ladanyi, 119,  9195 (2015). DOI:10.1021/jp509473z.

J. McCarty, A. Clark, J. Copperman, and M. G. Guenza “An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale” J. Chem. Phys. 140, 204913 (2014).

M. G. Guenza “Localization of Chain Dynamics in Entangled Polymer Melts” Phys. Rev. E 89, 052603 (2014).

E. de Lorimier, L. Coonrod, J. Copperman, A. Taber, E. Reister, K. Sharma, P. K. Todd, M. Guenza, J. A. Beglund “Modifications to toxic CUG RNAs induce structural stability and rescue missplicing in Myotonic Dystrophy” Nucleic Acid Res. 42, 12768 (2014).



Our research is supported in many ways by the National Science Foundation through the Chemistry Division (Theoretical Chemistry), the Division of Physics (Condensed Matter: Material Theory), and the computational effort is supported by the XSEDE program of NSF.

Our research has also been supported by the Petroleum Research Fund of the American Chemical Society and the University of Oregon.