Publication list of Raffaello Potestio

2021

• M. Giulini, M. Rigoli, G. Matiotti, R. Menichetti, T. Tarenzi, R. Fiorentini and R. Potestio, From system modelling to system analysis: the impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules, Front. Mol. Biosci. (2021)

• L. Tubiana, H. Kobayashi, R. Potestio, B. Duenweg, K. Kremer, P. Virnau and K. Daoulas, Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators, Journal of Physics: Condensed Matter (2021)

• F. Errica, M. Giulini, D. Bacciu, R. Menichetti, A. Micheli and R. Potestio, A deep graph network-enhanced sampling approach to efficiently explore the space of reduced representations of proteins, Front. Mol. Biosci. (2021) [arxiv preprint here]

• A. Baptista, R. Chandra Dutta, M. Sevilla, M. Heidari, R. Potestio, K. Kremer and R. Cortes-Huerto, Density-Functional-Theory Approach to the Hamiltonian Adaptive Resolution Simulation Method, Journal of Physics: Condensed Matter (2021)

2020

• M. Giulini, R. Menichetti, M. Scott Shell and R. Potestio, An information theory-based approach for optimal model reduction of biomolecules, J. Chem. Theor. Comput. (2020)

• R. Fiorentini, K. Kremer and R. Potestio, Ligand-protein interactions in lysozyme investigated through a dual-resolution model, Proteins (2020)

• M. Heidari, K. Kremer, R. Golestanian, R. Potestio, and R. Cortes-Huerto, Open-Boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations, J. Chem. Phys. (2020)

2019

• I. Tabujew, M. Heidari, C. Freidel, M. Helm, L. Tebbe, U. Wolfrum, K. Nagel-Wolfrum, K. Koynov, P. Biehl, F. H. Schacher, R. Potestio, and K. Peneva, Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental–Computational Approach, Biomacromolecules (2019)

• M. Heidari, R. Cortes-Huerto, R. Potestio, and K. Kremer, Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences, J. Chem. Phys. (2019)

• C. Perego and R. Potestio, Computational methods in the study of self-entangled proteins: a critical appraisal, Journal of Physics: Condensed Matter (2019)

• C. Perego and R. Potestio, Searching the Optimal Folding Routes of a Complex Lasso Protein, Biophysical Journal (2019)

• M. Giulini and R. Potestio, A deep learning approach to the structural analysis of proteins, Royal Society Interface Focus (2019)

• E. Riccardi, S. Pantano and R. Potestio, Envisioning data sharing for the biocomputing community, Royal Society Interface Focus (2019)

• R. Erban, S. Harris and R. Potestio, Multi-resolution simulations of intracellular processes, Royal Society Interface Focus (2019) [Introduction to the Interface Focus theme issue Multi-resolution simulations of intracellular processes organised by Radek Erban, Sarah Harris and Raffaello Potestio]

• T. Tarenzi , V. Calandrini, R. Potestio, and P. Carloni, Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor–Ligand Complexes, J. Chem. Theor. Comput. (2019)

• Diggins, C. Liu, M. Deserno, and R. Potestio, Optimal coarse-grained site selection in elastic network models of biomolecules, J. Chem. Theor. Comput. (2019)

2018

• M. Praprotnik, R. Cortes-Huerto, R. Potestio, L. Delle Site, Adaptive Resolution Molecular Dynamics Technique, Handbook of Materials Modeling: Methods: Theory and Modeling, 1-15 (2018)

• M. Heidari, K. Kremer, R. Cortes-Huerto and R. Potestio, Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids, J. Chem. Theor. Comput. (2018)

• M. Heidari, K. Kremer, R. Potestio and R. Cortes-Huerto, Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations, Molecular Physics, special issue in honour of Daan Frenkel, DOI: 10.1080/00268976.2018.1482429 (2018)

• M. Heidari, K. Kremer, R. Cortes-Huerto and R. Potestio, Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations, Eur. Phys. J. E 41:64 (2018) [JOURNAL HIGHLIGHT]

• M. Heidari, K. Kremer, R. Potestio and R. Cortes-Huerto, Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method, Entropy 20(4) (2018)

2017

• K. Kreis, K. Kremer, R. Potestio, M. E. Tuckerman, From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics, J. Chem. Phys. 147, 244104 (2017)

• H. Sharifi Dehsari, M. Heidari, A. Halda Ribeiro, W. Tremel, G. Jakob, D. Donadio, R. Potestio, and K. Asadi, Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles, Chem. Mater. 29 (22) (2017)

• T. Tarenzi, V. Calandrini, R. Potestio, A. Giorgetti, P. Carloni, Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme, J. Chem. Theory Comput. 13 (11) (2017)

• R. Fiorentini, K. Kremer, R. Potestio, and A. C. Fogarty, Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues, J. Chem. Phys. 146, 244113 (2017)

2016

• P. A. Netz, R. Potestio and K. Kremer, Adaptive resolution simulation of oligonucleotides, J. Chem. Phys. 145, 23 (2016)

• R. Cortes-Huerto, K. Kremer and R. Potestio, Communication: Kirkwood-Buff integrals in the thermodynamic limit from small-sized molecular dynamics simulations, J. Chem. Phys.145, 141103 (2016)

• A. C. Fogarty, R. Potestio and K. Kremer, A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site, Proteins: Structure, Function, and Bioinformatics, DOI: 10.1002/prot.25173 (2016) [Selected by Faculty of 1000]

• S. Najafi, R. Podgornik, R. Potestio and L. Tubiana, Role of Bending Energy and Knot Chirality in Knot Distribution and Their Effective Interaction along Stretched Semiflexible Polymers, Polymers 8 (10) (2016)

• K. Kreis and R. Potestio, The relative entropy is fundamental to adaptive resolution simulations, J. Chem. Phys. 145 (2016)

• S. Najafi, L. Tubiana, R. Podgornik and R. Potestio, Chirality modifies the interaction between knots, Europhys. Lett. 114 (5) (2016)

• M. Heidari, R. Cortes-Huerto, D. Donadio and R. Potestio, Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulation, Eur. Phys. J. Spec. Top. 225: 1505 (2016)

• K. Kreis, R. Potestio, K. Kremer and A. C. Fogarty, Adaptive resolution simulations with self-adjusting high-resolution regions, J. Chem. Theory Comput. 12 (8), 4067-4081 (2016) [cover article]

• J. M. Boereboom, R. Potestio, D. Donadio, and R. E. Bulo, Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials, J. Chem. Theory Comput. 12 (8), 3441-3448 (2016)

• K. Kreis, M. E. Tuckerman, D. Donadio, K. Kremer, and R. Potestio, From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations, J. Chem. Theory Comput. 12 (7), 3030-3039 (2016)

• R. Potestio and L. Tubiana, Discretized knot motion on a tensioned fiber induced by transverse waves, Soft Matter, 12, 669-673 (2015)

2015

• S. Najafi and R. Potestio, Folding of small knotted proteins: Insights from a mean field coarse-grained model, J. Chem. Phys. 143, 243121 (2015)

• S. Najafi and R. Potestio, Two Adhesive Sites Can Enhance the Knotting Probability of DNA, PLoS ONE 10(7): e0132132 (2015)

• A. C. Fogarty, R. Potestio, and K. Kremer, Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties, J. Chem. Phys. 142, 195101 (2015)

• K. Kreis, A. C. Fogarty, K. Kremer, R. Potestio, Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations, Eur. Phys. J. Special Topics, 224, 2289 (2015)

• P. Espanol, R. Delgado-Buscalioni, R. Everaers, R. Potestio, D. Donadio and K. Kremer, Statistical mechanics of Hamiltonian adaptive resolution simulations, J. Chem. Phys. 142, 064115 (2015)

2014

• K. Kreis, D. Donadio, K. Kremer and R. Potestio, A unified framework for force-based and energy-based adaptive resolution simulations, EuroPhysics Letters , 108(3) (2014)

• R. Potestio, Computer simulation of particles with position-dependent mass, The European Physical Journal B, 87:245 (2014)

• R. Potestio, C. Peter, and K. Kremer, Computer Simulations of Soft Matter: Linking the Scales, Entropy special issue "Molecular Dynamics Simulations" , 16(8), 4199-4245 (2014)

• S. Fritsch, R. Potestio, D. Donadio, and K. Kremer, Nuclear Quantum Effects in Water: A Multiscale Study, J. Chem. Theory Comput. , 10 (2), 816-824 (2014)

2013

• G. Polles, G. Indelicato, R. Potestio, P. Cermelli, R. Twarock, and C. Micheletti, Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition, PLoS Computational Biology 9(11): e1003331. doi: 10.1371/journal.pcbi.1003331 (2013) [cover article]

• R. Potestio, P. Español, R. Delgado-Buscalioni, R. Everaers, K. Kremer, and D. Donadio, Monte Carlo Adaptive Resolution Simulation of Multicomponent Molecular Liquids, Phys. Rev. Lett. 111, 060601 (2013)

• R. Potestio, S. Fritsch, P. Español, R. Delgado-Buscalioni, K. Kremer, R. Everaers, and D. Donadio,Hamiltonian Adaptive Resolution Simulation for Molecular Liquids, Phys. Rev. Lett. 110 , 108301 (2013)

• R. Potestio and K. Kremer, Theory and practice of adaptive resolution simulations, Proceedings of the HYBRID2013 workshop of the John von Neumann Institute for Computing, vol. 46 (2013)

2012

• G. Morra, R. Potestio, C. Micheletti and Giorgio Colombo, Corresponding functional dynamics across the Hsp90 chaperone family: insights from amultiscale analysis of MD simulations, PLoS Computational Biology 8(3): e1002433. doi:10.1371/journal.pcbi.1002433 (2012)

• R. Potestio and L. Delle Site, Quantum locality and equilibrium properties in low-temperature parahydrogen: a multiscale simulation study, J. Chem, Phys. 136(5), 054101 (2012)

2010

• R. Potestio, C. Micheletti and H. Orland, Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops, PlOS Computational Biology, 6(7) (2010) [Selected by Faculty of 1000]

• R. Potestio, F. Pontiggia, V. Carnevale and C. Micheletti, Bridging the atomic and coarse-grained descriptions of collective motions in proteins, invited contribution for the book Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies, edited by A. Kolinski, Springer (2010)

• R. Potestio , T. Aleksiev, F. Pontiggia , S. Cozzini , and C. Micheletti, ALADYN: a web server for aligning proteins by matching their large-scale motion, Nucleic Acids Research - Web Server Issue, doi:10.1093/nar/gkq293 (2010) [go to ALADYN webserver]

2009

• R. Potestio, F. Caccioli and P. Vivo, Random matrix approach to collective behavior and bulk universality in protein dynamics, Phys. Rev. Lett., 103, 268101 (2009)

• T. Aleksiev, R. Potestio , F. Pontiggia , S. Cozzini , and C. Micheletti, PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains, Bioinformatics, DOI 10.1093/bioinformatics/btp512 (2009) [go to PiSQRD webserver]

• R. Potestio, F. Pontiggia and C. Micheletti, Coarse-grained description of proteins' internal dynamics: an optimal strategy for decomposing proteins in rigid subunits, Biophys. J., 96, 4993-5002 (2009)