PhD THESIS
Pablo Romano – Ph.D. Defense: August 8, 2017 – ““Markov Models for the Conformational Kinetics in DNA Breathing Fluctuations”.
Jeremy T. Copperman – Ph.D. Defense: May 18, 2016 – “Diffusive and Activated Contributions in Protein Dynamics”
James Joseph McCarty – Ph.D. Defense: November 25, 2013 – “Multiscale Modeling and Thermodynamic Consistency between Soft-Particle Representations of Macromolecular Liquids”
Anthony Clark – Ph.D. Defense – March 4, 2013 – “Properties of Effective Pair Potentials that Map Polymer Melts onto Liquids of Soft Colloid Chains”
Ivan Lyubimov – Ph. D. Defense – May 16, 2012 – “Theoretical Reconstruction of the Structure and Dynamics of Polymer Melts from their Coarse-Grained Description”
Edward John Sambriski – Ph. D. Defense – November 2, 2006 – “Theoretical Models for the Coarse-Graining of Polymeric Liquids”
Esther Caballero-Manrique – Ph. D. Defense – October 19, 2006 – “A Langevin Equation Approach to Bridge Different Timescales of Relaxation in Protein Dynamics”
MAIN PUBLICATIONS (for full list look at Research Gate)
E. R. Beyerle, M. G. Guenza Kinetics analysis of ubiquitin local fluctuations with Markov state modeling of the LE4PD normal modes The Journal of Chemical Physics, 151, 164119(1-13) (2019) DOI: 10.1063/1.5123513. Invited article in the special topic on Markov Models of Molecular Kinetics.
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.
M. Dinpajooh, M. G. Guenza “Thermodynamic Consistency in the Structure-based Integral Equation Coarse-Grained Method” Polymers, 117, 282-286 (2017).
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).
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, 2491-2495 (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.224, 2177-2192 (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)
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. 2015) arXiv:1509.08546.
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 119, 9195-9211 (2015), Festschrift issue honoring Branka Ladanyi DOI:10.1021/jp509473z.
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 Research 42, 12768 (2014).
J. McCarty, A. Clark, J. Copperman, and M. G. Guenza “Accurate Determination of the Thermodynamic Properties of Polymer Melts from Highly Coarse-Grained Simulation and Theory” J. Chem. Phys. 140, 204913 (2014).
M. G. Guenza “Localization of Chain Dynamics in Entangled Polymer Melts” Phys. Rev. E 89, 052603 (2014).
A. Clark, J. McCarty, M. G. Guenza “Effective Potentials for Representing Polymers in Melts as Chains of Interacting Soft Particles” J. Chem. Phys. 139, 124906 (2013).
I. Y. Lyubimov, M.G. Guenza “Theoretical Reconstruction of Realistic Dynamics of Highly Coarse-Grained cis-1,4-Polybutadiene Melts” J. Chem. Phys. 138, 12A546 (2013).
J. McCarty, A. Clark, I. Y. Lyubimov, M. G. Guenza “Thermodynamic Consistency between Analytical Integral Equation Theory and Coarse-Grained Molecular Dynamics Simulations of Homopolymer Melts” Macromolecules 45, 8482-8493 (2012).
A. Clark, J. McCarty, I. Y. Lyubimov, M. G. Guenza “Thermodynamic consistency in variable-level coarse-graining of polymeric liquids” Physical Review Letters 109, 168301-5 (2012).
I. Y. Lyubimov, and M. G. Guenza “A First Principle Approach to Rescale the Dynamics of Simulated Coarse-Grained Macromolecular Liquids”, Physical Review E 84, 031801-19 (2011).
J. McCarty, and M. G. Guenza “Multiscale Modeling of Polymer Mixtures: Scale Bridging in the Athermal and Thermal Regime” Journal of Chemical Physics 133, 094904-15 (2010).
I. Y. Lyubimov, J. McCarty, A. Clark, and M. G. Guenza “Analytical Rescaling of Polymer Dynamics from Mesoscale Simulations” Journal of Chemical Physics 132, 2249031-5 (2010).
J. McCarty, I. Y. Lyubimov, and M. G. Guenza “Effective Soft-Core Potentials and Mesoscopic Simulations of Binary Polymer Mixtures” Macromolecules 43, 3964-3979 (2010).
A. J. Clark, and M. G. Guenza “Mapping of Polymer Melts onto Soft-Colloidal Chains Journal of Chemical Physics 132, 044902-12 (2010). This paper has been selected for the February 1, 2010 issue of Virtual Journal of Biological Physics Research at http://www.vjbio.org.
J. McCarty, I. Y. Lyubimov, and M. G. Guenza “Multi-Scale Modeling of Coarse-Grained Macromolecular Liquids”” Journal of Physical Chemistry B 113, 11876-11886 (2009).
M. Zamponi, A. Wischnewski, M. Monkenbusch, L. Willner, D. Richter, P. Falus, B. Farago, and M. G. Guenza “Cooperative Dynamics in Homopolymer Melts: a Comparison of Theoretical Predictions with Neutron Spin Echo Experiments” Journal of Physical Chemistry B 112, 16220-16229 (2008).
P.Debnath, M. G. Guenza “Cooperative Dynamics in Polymer Melts from the Unentangled to the Entangled regime” Philosophical Magazine 88, 33-35 (2008).
M. G. Guenza “Theoretical Models to Bridge Time Scales in Polymer Dynamics” invited review article Journal of Physics: Condensed Matter 20, 033101-0331024 (2008).
Esther Caballero-Manrique, Jenelly K. Brey, William A. Deutschman, Fredrick W. Dahlquist, and M. G. Guenza “A Theory of Protein Dynamics to Predict N.M.R. Relaxation” Biophysical Journal 93, 4128-4140 (2007).
E. J. Sambriski, and M. G. Guenza “Theoretical Coarse-Graining Approach to Bridge Length Scales in Diblock Copolymer Liquids” Physical Review E 76, 051801-13 (2007).
This paper has been selected for the November 12, 2007 issue of Virtual Journal of Nanoscience and Technology and the November 15, 2007 issue of Virtual Journal of Biological Physics Research.
E. J. Sambriski, G. Yatsenko, M. A. Nemiroskaya, and M. G. Guenza “Bridging Length Scales in Polymer Melt Relaxation for Macromolecules with Specific Local Structure” Journal of Physics: Condensed Matter 19, 205115-26 (2007).
E. J. Sambriski, G. Yatsenko, M. A. Nemiroskaya, and M. G. Guenza “An Analytical Coarse-Grained Description for Polymer Melts” Journal of Chemical Physics 125, 234902-12 (2006). This paper has been selected for the December 15, 2006 issue of Virtual Journal of Biological Physics Research at http://www.vjbio.org.
M. C. Fink, K. V. Adair, M. G. Guenza, and A. H. Marcus “Translational Diffusion of Fluorescent Proteins by Molecular Fourier Imaging Correlation Spectroscopy” Biophysical Journal 91, 3482-3498 (2006).
M. G. Guenza “Intermolecular Effects in the Dynamics of Polymer Melts: Interplay of Cooperative Dynamics and Entanglements” Proceedings of the Time of Polymer Conference, AIP Conference Proceedings 1255, 114-116 (2010).
E. Caballero-Manrique, M. G. Guenza “A Langevin Equation Approach to Bridge Different Timescales of Relaxation in Protein Dynamics”51st Annual Meeting of the Biophysical Society, MAR 03-07, 2007. Biophysical Journal 377A (2007).
G. Yatsenko, E. J. Sambriski, and M. G. Guenza “Coarse-Grained Description of Polymer Blends as Interacting Soft-Colloidal Particles” Journal of Chemical Physics 122, 054907 (2005). This paper has been selected for the February 1, 2005 issue of Virtual Journal of Biological Physics Research at http://www.vjbio.org.
G. Yatsenko, E. J. Sambriski, M. A. Nemirovskaya, and M. Guenza “Analytical Soft-Core Potentials for Macromolecular Fluids and Mixtures” Physical Review Letters 93, 2578031 (2004).
This paper has been selected for the December 17, 2004 issue of Virtual Journal of Nanoscience & Technology at http://www.vjnano.org and for the December 15, 2004 issue of Virtual Journal of Biological Physics Research at http://www.vjbio.org.
M. Guenza “Cooperative Dynamics in Semiflexibile Unentangled Polymer Fluids“, Journal of Chemical Physics 119, 7568 (2003). This paper has been selected for the October 1, 2003 issue of the Virtual Journal of Biological Physics Research at http://www.vjbio.org.
M. Knowles, R. A. Capaldi, M. Guenza, and A. H. Marcus “Cytoskeletal-Assisted Dynamics of the Mithocondrial Reticulum in Living cells”, Proceedings of the National Academy of Science 99, 14772 (2002).
M. Guenza “Intermolecular Effects in the Center-of-Mass Dynamics of Unentangled Polymer Fluids” Macromolecules, 35, 2714 (2002).
M. Guenza “Cooperative Dynamics in Unentangled Polymer Fluids” Physical Review Letters, 88, 25901 (2002).
M. Guenza “Cooperative Dynamics in Polymer Liquids” American Chemical Society Volume on Liquid Dynamics: Experiment, Simulation and Theory 92 (2002) J. T. Fourkas Ed. (refereed publication).
M. Guenza “Many Chain Correlated Dynamics in Polymer Fluids” Journal of Chemical Physics, 110, 7574 (1999).
M. Guenza, K. S. Schweizer “Mode-Coupling Theory of Self Diffusion in Diblock Copolymer: II Comparison with Experimental Data” Journal of Chemical Physics, 108, 1271 (1998).
M. Guenza, K. S. Schweizer “Mode-Coupling Theory of Self Diffusion in Diblock Copolymer: II Comparison with Experimental Data” Journal of Chemical Physics, 108, 1271 (1998).
M. Guenza, H. Tang, K. S. Schweizer “Mode-Coupling Theory of Self-Diffusion in Diblock Copolymer: I General Derivation and Qualitative Predictions.” Journal of Chemical Physics, 108, 1257 (1998).
M. Guenza, H. Tang, K. S. Schweizer “Mode-Coupling Theory of Self-Diffusion in Diblock Copolymer: I General Derivation and Qualitative Predictions.” Journal of Chemical Physics, 108, 1257 (1998).
M. Guenza, K. S. Schweizer “Local and Microdomain Concentration Fluctuation Effects in Block Copolymer solutions.” Macromolecules, 30, 4205 (1997).
K. S. Schweizer, M. Fuchs, G.Szamel, M.Guenza, H.Tang “Mode-Coupling Theory of the Dynamics of Entangled Macromolecular Fluids” Macromolecular Theory and Simulations, 6, 1037 (1997).
M. Guenza, H. Tang, K. S. Schweizer “Suppression of Entangled Diblock Copolymer Diffusion at and below the Order-Disorder Transition.” Macromolecules 30, 3423 (1997).
M. Guenza, K. S. Schweizer “Fluctuation Effects in Diblock Copolymer Fluids: Comparison of Theories and Experiments. “ Journal of Chemical Physics, 106, 7391 (1997).
M. Guenza, K.F.Freed “A Rotational Isomeric State Approach to the Long Time Dynamics of Low Molecular Weight Polymers.” Journal of Chemical Physics 105, 3823 (1996).
A. Ziabicki, L. Jarecki, A. Perico, M. Guenza “Orientational Relaxation Times of Worm- Like Chains.” Macromolar Theory and Simulations 4, 643 (1995).
A.Perico, M. Guenza, M. Mormino, R. Fioravanti “Protein Dynamics: Rotational Diffusion of Rigid and Fluctuating Three Dimensional Structures.” Biopolymers, 35, 47 (1995).
M. Guenza, A. Perico “Local Dynamics and Structural Investigation of Star Polymers.” Invited review article -Trends in Polymers Science, Elsevier Trends Journal, February 1994, Vol.2, No.2, Cambridge, UK.
M. Guenza, A.Perico “Dynamics of Star Polymers”. Macromolecular Symposia 81, 115 (1994).
M. Guenza, A.Perico “A Reduced Description of the Local Dynamics of Star Polymers.” Macromolecular Reports, A31 (suppls. 6&7), 1274 (1994).
A.Perico, M.Mormino, M. Guenza “Models for Long Time Protein Dynamics.” Macromolecular Reports, A31 (suppls. 6&7), 1009 (1994).
M. Guenza, A.Perico “Static and Dynamic Structure Factors for Star Polymers in Theta Conditions.” Macromolecules, 26, 4196 (1993).
L. Carpaneto, G. Costa, E. Marsano, M.Guenza, B. Valenti “Thermotropicity of Fully- Aromatic Polyesters Based on 3,4’-dicarboxydiphenil ether.” Polymers for Advanced Technologies, 4, 367 (1992).
M. Guenza, A.Perico “A Reduced Description of the Local Dynamics of Star Polymers.” Macromolecules, 25, 5942 (1992).
M. Guenza, M. Mormino, A. Perico “A Local Approach to the Dynamics of Star Polymers.” Macromolecules 24, 6168 (1991).
M. Alloisio, M. Guenza, C. Cuniberti “Solution Conformation of DNA as Probed by Ethidium Fluorescence.” in “Spectroscopy of Biological Molecules”, p.359, edited by R.E.Hester and R.B.Girling, York, UK (1991).
M. Guenza, C. Cuniberti “Environment-Induced Changes in DNA Conformation as Probed by Ethidium Bromide Fluorescence.” Biophysical Chemistry 38, 11 (1990).
M. Guenza, C. Cuniberti “The Ethidium Bromide Dimer. Absorption and Fluorescence Properties in Aqueous Solutions.” Spectrochimica Acta, 44A, 1359 (1988).
A. Perico, M. Guenza “Viscoelastic Relaxation of Segment Orientation in Dilute Polymer Solutions II. Stiffness Dependence of Fluorescence Polarization.” Journal of Chemical Physics 84, 510 (1986).
A. Perico, M. Guenza “Viscoelastic Relaxation of Segment Orientation in Dilute Polymer Solutions’’ Journal of Chemical Physics 83, 3103 (1985).