Publications of Raffaello Potestio

Signorini, L. F.; Perego, C.; Potestio, R.: Protein self-entanglement modulates successful folding to the native state: A multi-scale modeling study. The Journal of Chemical Physics 155 (11), 115101 (2021)

Tubiana, L.; Kobayashi, H.; Potestio, R.; Dünweg, B.; Kremer, K.; Virnau, P.; Daoulas, K.: Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators. Journal of Physics: Condensed Matter 33 (20), 204003 (2021)

Baptista, L. A.; Dutta, R. C.; Sevilla, M.; Heidari, M.; Potestio, R.; Kremer, K.; Cortes Huerto, R.: Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method. Journal of Physics: Condensed Matter 33 (18), 184003 (2021)

Fiorentini, R.; Kremer, K.; Potestio, R.: Ligand-protein interactions in lysozyme investigated through a dual-resolution model. Proteins: Structure, Function, and Bioinformatics 88 (10), pp. 1351 - 1360 (2020)

Heidari, M.; Kremer, K.; Golestanian, R.; Potestio, R.; Cortes Huerto, R.: Open-boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations. The Journal of Chemical Physics 152 (19), 194104 (2020)

Heidari, M.; Cortes Huerto, R.; Potestio, R.; Kremer, K.: Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences. The Journal of Chemical Physics 151 (14), 144105 (2019)

Perego, C.; Potestio, R.: Computational methods in the study of self-entangled proteins: a critical appraisal. Journal of Physics: Condensed Matter 31 (44), 443001 (2019)

Tabujew, I.; Heidari, M.; Freidel, C.; Helm, M.; Tebbe, L.; Wolfrum, U.; Nagel-Wolfrum, K.; Koynov, K.; Biehl, P.; Schacher, F. H. et al.; Potestio, R.; Peneva, K.: Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental-Computational Approach. Biomacromolecules 20 (12), pp. 4389 - 4406 (2019)

Heidari, M.; Cortes-Huerto, R.; Kremer, K.; Potestio, R.: Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations. European Physical Journal E 41 (5), 64 (2018)

Heidari, M.; Kremer, K.; Cortes-Huerto, R.; Potestio, R.: Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids. Journal of Chemical Theory and Computation 14 (7), pp. 3409 - 3417 (2018)

Heidari, M.; Kremer, K.; Potestio, R.; Cortes-Huerto, R.: Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method. Entropy 20 (4), 222 (2018)

Heidari, M.; Kremer, K.; Potestio, R.; Cortes-Huerto, R.: Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations. Molecular Physics 116 (21-22), pp. 3301 - 3310 (2018)

Fiorentini, R.; Kremer, K.; Potestio, R.; Fogarty, A. C.: Using force-based adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues. The Journal of Chemical Physics 146 (24), 244113 (2017)

Fogarty, A. C.; Potestio, R.; Kremer, K.: Erratum: “Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties” [J. Chem. Phys. 142, 195101 (2015)]. The Journal of Chemical Physics 146 (4), 049901 (2017)

Kreis, K.; Kremer, K.; Potestio, R.; Tuckerman, M. E.: From classical to quantum and back: Hamiltonian adaptive resolution path integral, ring polymer, and centroid molecular dynamics. The Journal of Chemical Physics 147 (24), 244104 (2017)

Sharifi Dehsari, H.; Heidari, M.; Halda Ribeiro, A.; Tremel, W.; Jakob, G.; Donadio, D.; Potestio, R.; Asadi, K.: Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles. Chemistry of Materials 29 (22), pp. 9648 - 9656 (2017)

Tarenzi, T.; Calandrini, V.; Potestio, R.; Giorgetti, A.; Carloni, P.: Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme. Journal of Chemical Theory and Computation 13 (11), pp. 5647 - 5657 (2017)

Boereboom, J. M.; Potestio, R.; Donadio, D.; Bulo, R. E.: Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials. Journal of Chemical Theory and Computation 12 (8), pp. 3441 - 3448 (2016)

Cortes Huerto, R.; Kremer, K.; Potestio, R.: Communication: Kirkwood-Buff integrals in the thermodynamic limit from small-sized molecular dynamics simulations. The Journal of Chemical Physics 145 (14), 141103 (2016)

Fogarty, A. C.; Potestio, R.; Kremer, K.: 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 84 (12), pp. 1902 - 1913 (2016)