Marina G. Guenza - Publications

Affiliations: 
Department of Physics University of Oregon, Eugene, OR, United States 
Area:
General Physics, Physical Chemistry

49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Beyerle ER, Dinpajooh M, Ji H, von Hippel PH, Marcus AH, Guenza MG. Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms. Nucleic Acids Research. PMID 33503257 DOI: 10.1093/nar/gkab015  1
2019 Beyerle ER, Guenza MG. Kinetics analysis of ubiquitin local fluctuations with Markov state modeling of the LE4PD normal modes. The Journal of Chemical Physics. 151: 164119. PMID 31675886 DOI: 10.1063/1.5123513  1
2019 Dinpajooh M, Guenza MG. Correction to "On the Density Dependence of the Integral Equation Coarse-Graining Effective Potential". The Journal of Physical Chemistry. B. 123: 2466. PMID 30821979 DOI: 10.1021/acs.jpcb.9b01664  1
2019 Dinpajooh M, Guenza MG. Can pure polymer liquids be represented at two different resolutions simultaneously? The Journal of Chemical Physics. 151: 061102. DOI: 10.1063/1.5115791  0.01
2018 Guenza MG, Dinpajooh M, McCarty J, Lyubimov IY. Accuracy, Transferability, and Efficiency of Coarse-Grained Models of Molecular Liquids. The Journal of Physical Chemistry. B. 122: 10257-10278. PMID 30153027 DOI: 10.1021/acs.jpcb.8b06687  0.01
2018 Dinpajooh M, Guenza MG. Coarse-graining simulation approaches for polymer melts: the effect of potential range on computational efficiency. Soft Matter. PMID 30070292 DOI: 10.1039/c8sm00868j  1
2018 Beyerle ER, Guenza M. A Comparison of Collective Coordinates for Analyzing Protein Dynamics Biophysical Journal. 114: 232a-233a. DOI: 10.1016/j.bpj.2017.11.1294  0.01
2017 Dinpajooh M, Guenza MG. On the Density Dependence of the Integral Equation Coarse-Graining Effective Potential. The Journal of Physical Chemistry. B. PMID 29144758 DOI: 10.1021/acs.jpcb.7b10494  1
2017 Copperman J, Dinpajooh M, Beyerle ER, Guenza MG. Universality and Specificity in Protein Fluctuation Dynamics. Physical Review Letters. 119: 158101. PMID 29077439 DOI: 10.1103/PhysRevLett.119.158101  1
2017 Romano PG, Guenza MG. GRadient Adaptive Decomposition (GRAD) Method: Optimized Refinement Along Macrostate Borders in Markov State Models. Journal of Chemical Information and Modeling. 57: 2729-2740. PMID 29035546 DOI: 10.1021/acs.jcim.7b00261  0.01
2017 deLorimier E, Hinman MN, Copperman J, Datta K, Guenza M, Berglund JA. Pseudouridine modification inhibits muscleblind-like 1 (MBNL1) binding to CCUG repeats and minimally structured RNA through reduced RNA flexibility. The Journal of Biological Chemistry. PMID 28130447 DOI: 10.1074/jbc.M116.770768  1
2016 Ozog D, Malony AD, Guenza M. The UA?CG Workflow: High Performance Molecular Dynamics of Coarse-Grained Polymers Proceedings - 24th Euromicro International Conference On Parallel, Distributed, and Network-Based Processing, Pdp 2016. 272-279. DOI: 10.1109/PDP.2016.127  1
2016 Copperman J, Guenza MG. Mode localization in the cooperative dynamics of protein recognition Journal of Chemical Physics. 145. DOI: 10.1063/1.4954506  1
2016 Jose D, Michael MM, Romano P, Camel BR, Meze KH, Johnson NP, Guenza M, Marcus AH, von Hippel PH. Binding of the Single-Stranded DNA Binding Protein (gp32) of T4 Bacteriophage Induces Position-Specific Local Conformational Changes in DNA Lattices that can be Monitored by Fluorescent Probes Biophysical Journal. 110: 239a. DOI: 10.1016/J.BPJ.2015.11.1316  0.01
2015 Clark AJ, McCarty J, Guenza MG. Comment on "Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study" [J. Chem. Phys. 142, 054905 (2015)]. The Journal of Chemical Physics. 143: 067101. PMID 26277169 DOI: 10.1063/1.4928457  1
2015 Copperman J, Guenza MG. Coarse-Grained Langevin Equation for Protein Dynamics: Global Anisotropy and a Mode Approach to Local Complexity Journal of Physical Chemistry B. 119: 9195-9211. PMID 25356856 DOI: 10.1021/jp509473z  1
2015 Guenza MG. Advancements in multi scale modeling: Adaptive resolution simulations and related issues European Physical Journal: Special Topics. 224: 2491-2495. DOI: 10.1140/epjst/e2015-02529-1  1
2015 Guenza MG. Structural and thermodynamic consistency in coarse-grained models of macromolecules Journal of Physics: Conference Series. 640. DOI: 10.1088/1742-6596/640/1/012009  1
2015 Copperman J, Guenza MG. Predicting protein dynamics from structural ensembles Journal of Chemical Physics. 143. DOI: 10.1063/1.4935575  1
2015 Ozog D, McCarty J, Gossett G, Malony AD, Guenza M. Fast equilibration of coarse-grained polymeric liquids Journal of Computational Science. 9: 33-38. DOI: 10.1016/j.jocs.2015.04.015  1
2014 Guenza MG. Localization of chain dynamics in entangled polymer melts Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 89. PMID 25353822 DOI: 10.1103/PhysRevE.89.052603  1
2014 deLorimier E, Coonrod LA, Copperman J, Taber A, Reister EE, Sharma K, Todd PK, Guenza MG, Berglund JA. Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model. Nucleic Acids Research. 42: 12768-78. PMID 25303993 DOI: 10.1093/nar/gku941  1
2014 McCarty J, Clark AJ, Copperman J, Guenza MG. An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale. The Journal of Chemical Physics. 140: 204913. PMID 24880331 DOI: 10.1063/1.4875923  1
2014 Guenza MG. Entangled dynamics of polyethylene melts and tracer dynamics Aip Conference Proceedings. 1599: 22-25. DOI: 10.1063/1.4876768  1
2013 Clark AJ, McCarty J, Guenza MG. Effective potentials for representing polymers in melts as chains of interacting soft particles. The Journal of Chemical Physics. 139: 124906. PMID 24089803 DOI: 10.1063/1.4821818  1
2013 Lyubimov IY, Guenza MG. Theoretical reconstruction of realistic dynamics of highly coarse-grained cis-1,4-polybutadiene melts. The Journal of Chemical Physics. 138: 12A546. PMID 23556797 DOI: 10.1063/1.4792367  1
2013 Copperman JT, Guenza MG. In Silico Insight into Transitional Structures and Barrier-Crossing Dynamics of DNA and RNA Oligomers Biophysical Journal. 104: 199a. DOI: 10.1016/j.bpj.2012.11.1122  0.01
2012 Clark AJ, McCarty J, Lyubimov IY, Guenza MG. Thermodynamic consistency in variable-level coarse graining of polymeric liquids. Physical Review Letters. 109: 168301. PMID 23215138 DOI: 10.1103/PhysRevLett.109.168301  1
2012 McCarty J, Clark AJ, Lyubimov IY, Guenza MG. Thermodynamic consistency between analytic integral equation theory and coarse-grained molecular dynamics simulations of homopolymer melts Macromolecules. 45: 8482-8493. DOI: 10.1021/ma301502w  1
2011 Lyubimov I, Guenza MG. First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 84. DOI: 10.1103/PhysRevE.84.031801  1
2010 Lyubimov IY, McCarty J, Clark A, Guenza MG. Analytical rescaling of polymer dynamics from mesoscale simulations. The Journal of Chemical Physics. 132: 224903. PMID 20550415 DOI: 10.1063/1.3450301  1
2010 McCarty J, Guenza MG. Multiscale modeling of binary polymer mixtures: Scale bridging in the athermal and thermal regime Journal of Chemical Physics. 133. DOI: 10.1063/1.3483236  1
2010 Guenza MG. Intermolecular effects in the dynamics of polymer melts: Interplay of cooperative dynamics and entanglements Aip Conference Proceedings. 1255: 114-116. DOI: 10.1063/1.3455548  1
2010 Clark AJ, Guenza MG. Mapping of polymer melts onto liquids of soft-colloidal chains Journal of Chemical Physics. 132. DOI: 10.1063/1.3292013  1
2010 McCarty J, Lyubimov IY, Guenza MG. Effective soft-core potentials and mesoscopic simulations of binary polymer mixtures Macromolecules. 43: 3964-3979. DOI: 10.1021/ma100052z  1
2009 McCarty J, Lyubimov IY, Guenza MG. Multiscale modeling of coarse-grained macromolecular liquids. The Journal of Physical Chemistry. B. 113: 11876-86. PMID 19678631 DOI: 10.1021/jp905071w  1
2008 Zamponi M, Wischnewski A, Monkenbusch M, Willner L, Richter D, Falus P, Farago B, Guenza MG. Cooperative dynamics in homopolymer melts: a comparison of theoretical predictions with neutron spin echo experiments. The Journal of Physical Chemistry. B. 112: 16220-9. PMID 19072142 DOI: 10.1021/jp807035z  1
2008 Guenza MG. Theoretical models for bridging timescales in polymer dynamics Journal of Physics Condensed Matter. 20. DOI: 10.1088/0953-8984/20/03/033101  1
2008 Debnath P, Guenza MG. Cooperative dynamics in polymer melts from the unentangled to the entangled regime Philosophical Magazine. 88: 4131-4136. DOI: 10.1080/14786430802464255  1
2007 Sambriski EJ, Guenza MG. Theoretical coarse-graining approach to bridge length scales in diblock copolymer liquids. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 051801. PMID 18233675 DOI: 10.1103/PhysRevE.76.051801  1
2007 Caballero-Manrique E, Bray JK, Deutschman WA, Dahlquist FW, Guenza MG. A theory of protein dynamics to predict NMR relaxation. Biophysical Journal. 93: 4128-40. PMID 17766356 DOI: 10.1529/biophysj.107.111849  1
2007 Sambriski EJ, Yatsenko G, Nemirovskaya MA, Guenza MG. Bridging length scales in polymer melt relaxation for macromolecules with specific local structures Journal of Physics Condensed Matter. 19. DOI: 10.1088/0953-8984/19/20/205115  1
2006 Sambriski EJ, Yatsenko G, Nemirovskaya MA, Guenza MG. Analytical coarse-grained description for polymer melts. The Journal of Chemical Physics. 125: 234902. PMID 17190572 DOI: 10.1063/1.2404669  1
2006 Fink MC, Adair KV, Guenza MG, Marcus AH. Translational diffusion of fluorescent proteins by molecular fourier imaging correlation spectroscopy. Biophysical Journal. 91: 3482-98. PMID 16920833 DOI: 10.1529/biophysj.106.085712  1
2005 Yatsenko G, Sambriski EJ, Guenza MG. Coarse-grained description of polymer blends as interacting soft-colloidal particles. The Journal of Chemical Physics. 122: 54907. PMID 15740353 DOI: 10.1063/1.1835271  1
2004 Yatsenko G, Sambriski EJ, Nemirovskaya MA, Guenza M. Analytical soft-core potentials for macromolecular fluids and mixtures. Physical Review Letters. 93: 257803. PMID 15697944 DOI: 10.1103/PhysRevLett.93.257803  1
2002 Knowles MK, Guenza MG, Capaldi RA, Marcus AH. Cytoskeletal-assisted dynamics of the mitochondrial reticulum in living cells. Proceedings of the National Academy of Sciences of the United States of America. 99: 14772-7. PMID 12417764 DOI: 10.1073/pnas.232346999  1
2002 Guenza MG. Cooperative dynamics in polymer liquids Acs Symposium Series. 820: 92-105.  1
2001 Guenza M. Cooperative dynamics in unentangled polymer fluids. Physical Review Letters. 88: 025901. PMID 11801026 DOI: 10.1103/PhysRevLett.88.025901  0.28
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