Publications

(1) Coluzza, I.; SPRIK, M.; Ciccotti, G. Constrained Reaction Coordinate Dynamics for Systems with Constraints. Mol. Phys. 2003, 101 (18), 2885–2894. https://doi.org/10.1080/00268970310001592746.

(2) Coluzza, I.; Muller, H. G. G.; Frenkel, D. Designing Refoldable Model Molecules. Phys. Rev. E 2003, 68 (4), 46703. https://doi.org/10.1103/PhysRevE.68.046703.

(3) Coluzza, I.; Frenkel, D. Designing Specificity of Protein-Substrate Interactions. Phys. Rev. E - Stat. Nonlinear, Soft Matter Phys. 2004, 70 (5 1), 51917. https://doi.org/10.1103/PhysRevE.70.051917.

(4) Coluzza, I.; Frenkel, D. Virtual‐Move Parallel Tempering. ChemPhysChem 2005, 6 (9), 1779–1783.

(5) Coluzza, I.; Frenkel, D. Virtual-Move Parallel Tempering. ChemPhysChem 2005, 6 (9), 1779–1783. https://doi.org/10.1002/cphc.200400629.

(6) Coluzza, I.; Van Der Vies, S. M.; Frenkel, D. Translocation Boost Protein-Folding Efficiency of Double-Barreled Chaperonins. Biophys. J. 2006, 90 (10), 3375–3381. https://doi.org/10.1529/biophysj.105.074898.

(7) Coluzza, I.; Frenkel, D. Monte Carlo Study of Substrate-Induced Folding and Refolding of Lattice Proteins. Biophys. J. 2007, 92 (4), 1150–1156. https://doi.org/10.1529/biophysj.106.084236.

(8) Coluzza, C.; Bicchieri, M.; Monti, M.; Piantanida, G.; Sodo, A. Atomic Force Microscopy Application for Degradation Diagnostics in Library Heritage. Surf. Interface Anal. 2008, 40 (9), 1248–1253.

(9) Rubenstein, B. M.; Miller, M. A.; Coluzza, I. Influence of Entropic Frustration upon Protein Binding and Self-Assembly. In Abstracts of Papers, 236th ACS National Meeting, Philadelphia, PA, United States, August 17-21, 2008; AMER CHEMICAL SOC 1155 16TH ST, NW, WASHINGTON, DC 20036 USA, 2008; Vol. 236, p PHYS-493.

(10) Coluzza, I.; De Simone, A.; Fraternali, F.; Frenkel, D. Multi-Scale Simulations Provide Supporting Evidence for the Hypothesis of Intramolecular Protein Translocation in GroEL/GroES Complexes. PLoS Comput. Biol. 2008, 4 (2), e1000006. https://doi.org/10.1371/journal.pcbi.1000006.

(11) Coluzza, I.; Hansen, J. P. J.-P. J.-P. Transition from Highly to Fully Stretched Polymer Brushes in Good Solvent. Phys. Rev. Lett. 2008, 100 (1), 016104. https://doi.org/10.1103/PhysRevLett.100.016104.

(12) Capone, B.; Hansen, J.-P.; Coluzza, I. Competing Micellar and Cylindrical Phases in Semi-Dilute Diblock Copolymer Solutions. Soft Matter 2010, 6 (24), 6075. https://doi.org/10.1039/c0sm00738b.

(13) Coluzza, I.; Capone, B.; Hansen, J.-P. Rescaling of Structural Length Scales for “Soft Effective Segment” Representations of Polymers in Good Solvent. Soft Matter 2011, 7 (11). https://doi.org/10.1039/c1sm05335c.

(14) Coluzza, I. A Coarse-Grained Approach to Protein Design: Learning from Design to Understand Folding. PLoS One 2011, 6 (7), e20853. https://doi.org/10.1371/journal.pone.0020853.

(15) Capone, B.; Coluzza, I.; Hansen, J.-P. A Systematic Coarse-Graining Strategy for Semi-Dilute Copolymer Solutions: From Monomers to Micelles. J. Phys. Condens. Matter 2011, 23 (19), 194102. https://doi.org/10.1088/0953-8984/23/19/194102.

(16) Coluzza, I.; Capone, B.; Hansen, J.-P. J.-P. Rescaling of Structural Length Scales for “Soft Effective Segment” Representations of Polymers in Good Solvent. Soft Matter 2011, 7 (11), 5255. https://doi.org/10.1039/c1sm05335c.

(17) Coluzza, I.; Dellago, C. The Configurational Space of Colloidal Patchy Polymers with Heterogeneous Sequences. J. Phys. Condens. Matter 2012, 24 (28), 284111. https://doi.org/10.1088/0953-8984/24/28/284111.

(18) Coluzza, I.; MacDonald, J. T.; Sadowski, M. I.; Taylor, W. R.; Goldstein, R. a. Analytic Markovian Rates for Generalized Protein Structure Evolution. PLoS One 2012, 7 (5), e34228. https://doi.org/10.1371/journal.pone.0034228.

(19) Rubenstein, B. M.; Coluzza, I.; Miller, M. A. Controlling the Folding and Substrate-Binding of Proteins Using Polymer Brushes. Phys. Rev. Lett. 2012, 108 (20), 208104. https://doi.org/10.1103/PhysRevLett.108.208104.

(20) Coluzza, I.; van Oostrum, P. D. J.; Capone, B.; Reimhult, E.; Dellago, C. Design and Folding of Colloidal Patchy Polymers. Soft Matter 2012, DOI (3), 10.1039/c2sm26967h. https://doi.org/10.1039/c2sm26967h.

(21) Capone, B.; Coluzza, I.; Loverso, F.; Likos, C. N.; Blaak, R.; Lo Verso, F.; Likos, C. N.; Blaak, R.; Loverso, F.; Likos, C. N.; et al. Telechelic Star Polymers as Self-Assembling Units from the Molecular to the Macroscopic Scale. Phys. Rev. Lett. 2012, 109 (23), 238301. https://doi.org/10.1103/PhysRevLett.109.238301.

(22) Capone, B.; Coluzza, I.; Loverso, F.; Likos, C. N.; Blaak, R. Erratum: Telechelic Star Polymers as Self-Assembling Units from the Molecular to the Macroscopic Scale (Physical Review Letters (2012) 109 (238301)). Phys. Rev. Lett. 2013, 110 (3). https://doi.org/10.1103/PhysRevLett.110.039904.

(23) Capone, B.; Coluzza, I.; LoVerso, F.; Likos, C. N.; Blaak, R. Publisher’s Note: Telechelic Star Polymers as Self-Assembling Units from the Molecular to the Macroscopic Scale [Phys. Rev. Lett. 109, 238301 (2012)]. Phys. Rev. Lett. 2013, 110 (3), 39904.

(24) Coluzza, I.; Van Oostrum, P. D. J.; Capone, B.; Reimhult, E.; Dellago, C. Sequence Controlled Self-Knotting Colloidal Patchy Polymers. Phys. Rev. Lett. 2013, 110 (7), 075501. https://doi.org/10.1103/PhysRevLett.110.075501.

(25) Capone, B.; Coluzza, I.; Blaak, R.; Lo Verso, F.; Likos, C. N.; Verso, F. Lo; Likos, C. N.; Lo Verso, F.; Likos, C. N.; Verso, F. Lo; et al. Hierarchical Self-Assembly of Telechelic Star Polymers: From Soft Patchy Particles to Gels and Diamond Crystals. New J. Phys. 2013, 15 (9), 095002. https://doi.org/10.1088/1367-2630/15/9/095002.

(26) Coluzza, I.; Pisignano, D.; Gentili, D.; Pontrelli, G.; Succi, S. Ultrathin Fibers from Electrospinning Experiments under Driven Fast-Oscillating Perturbations. Phys. Rev. Appl. 2014, 2 (5), 54011. https://doi.org/10.1103/PhysRevApplied.2.054011.

(27) Pontrelli, G.; Gentili, D.; Coluzza, I.; Pisignano, D.; Succi, S. Effects of Non-Linear Rheology on Electrospinning Process: A Model Study. Mech. Res. Commun. 2014, 61, 41–46. https://doi.org/10.1016/j.mechrescom.2014.07.003.

(28) Coluzza, I. Transferable Coarse-Grained Potential for de Novo Protein Folding and Design. PLoS One 2014, 9(12), e112852. https://doi.org/10.1371/journal.pone.0112852.

(29) Lauricella, M.; Pontrelli, G.; Coluzza, I.; Pisignano, D.; Succi, S. The JETSPIN User Manual (Version 1.20). ArXiv e-prints 2015.

(30) Lauricella, M.; Pontrelli, G.; Coluzza, I.; Pisignano, D.; Succi, S. Different Regimes of the Uniaxial Elongation of Electrically Charged Viscoelastic Jets Due to Dissipative Air Drag. Mech. Res. Commun. 2015, 69, 97–102. https://doi.org/10.1016/j.mechrescom.2015.06.014.

(31) Coluzza, I.; Jackson, S. E.; Micheletti, C.; Miller, M. A. Knots in Soft Condensed Matter. J. Phys. Condens. Matter2015, 27 (35), 301. https://doi.org/10.1088/0953-8984/27/35/350301.

(32) Coluzza, I. Constrained versus Unconstrained Folding Free-Energy Landscapes. Mol. Phys. 2015, 113 (17–18), 2905–2912. https://doi.org/10.1080/00268976.2015.1043031.

(33) Lauricella, M.; Pontrelli, G.; Coluzza, I.; Pisignano, D.; Succi, S. JETSPIN: A Specific-Purpose Open-Source Software for Simulations of Nanofiber Electrospinning. Comput. Phys. Commun. 2015, 197, 227–238. https://doi.org/10.1016/j.cpc.2015.08.013.

(34) Coluzza, I. Computational Protein Design: A Review. J. Phys. Condens. Matter 2017, 29 (14), 143001. https://doi.org/10.1088/1361-648X/aa5c76.

(35) Coluzza, I.; Creamean, J.; Rossi, M.; Wex, H.; Alpert, P.; Bianco, V.; Boose, Y.; Dellago, C.; Felgitsch, L.; Fröhlich-Nowoisky, J.; et al. Perspectives on the Future of Ice Nucleation Research: Research Needs and Unanswered Questions Identified from Two International Workshops. Atmosphere (Basel). 2017, 8 (8), 138. https://doi.org/10.3390/atmos8080138.

(36) Bianco, V.; Pagès-Gelabert, N.; Coluzza, I.; Franzese, G. How the Stability of a Folded Protein Depends on Interfacial Water Properties and Residue-Residue Interactions. J. Mol. Liq. 2017, 245, 129–139. https://doi.org/10.1016/j.molliq.2017.08.026.

(37) Cardelli, C.; Bianco, V.; Rovigatti, L.; Nerattini, F.; Tubiana, L.; Dellago, C.; Coluzza, I. The Role of Directional Interactions in the Designability of Generalized Heteropolymers. Sci. Rep. 2017, 7 (1), 4986. https://doi.org/10.1038/s41598-017-04720-7.

(38) Bianco, V.; Franzese, G.; Dellago, C.; Coluzza, I. Role of Water in the Selection of Stable Proteins at Ambient and Extreme Thermodynamic Conditions. Phys. Rev. X 2017, 7 (2), 021047. https://doi.org/10.1103/PhysRevX.7.021047.

(39) Bianchi, E.; Capone, B.; Coluzza, I.; Rovigatti, L.; van Oostrum, P. D. J. D. J. Limiting the Valence: Advancements and New Perspectives on Patchy Colloids, Soft Functionalized Nanoparticles and Biomolecules. Phys. Chem. Chem. Phys. 2017, 19 (30), 19847–19868. https://doi.org/10.1039/C7CP03149A.

(40) Cardelli, C.; Bianco, V.; Rovigatti, L.; Nerattini, F.; Tubiana, L.; Dellago, C.; Coluzza, I. Universal Criterion for Designability of Heteropolymers. Sci. Rep. 2017.

(41) Nerattini, F.; Tubiana, L.; Cardelli, C.; Bianco, V.; Dellago, C.; Coluzza, I. Protein Design under Competition for Amino Acids Availability. bioRxiv 2018. https://doi.org/doi.org/10.1101/331736.

(42) Cardelli, C.; Tubiana, L.; Bianco, V.; Nerattini, F.; Dellago, C.; Coluzza, I. Heteropolymer Design and Folding of Arbitrary Topologies Reveals an Unexpected Role of Alphabet Size on the Knot Population. Macromolecules2018, 51 (21), 8346–8356. https://doi.org/10.1021/acs.macromol.8b01359.

(43) Tubiana, L.; Jurásek, M.; Coluzza, I. Implementing Efficient Concerted Rotations Using Mathematica and C Code⋆. Eur. Phys. J. E 2018, 41 (7), 87. https://doi.org/10.1140/epje/i2018-11694-7.

(44) Mair, A.; Tung, C.; Cacciuto, A.; Coluzza, I. Translocation of a Globular Polymer through a Hairy Pore. J. Mol. Liq. 2018, 265, 603–610. https://doi.org/10.1016/j.molliq.2018.06.009.

(45) Nerattini, F.; Tubiana, L.; Cardelli, C.; Bianco, V.; Dellago, C.; Coluzza, I. Design of Protein − Protein Binding Sites Suggests a Rationale for Naturally Occurring Contact Areas. J. Chem. Theory Comput. 2018. https://doi.org/10.1021/acs.jctc.8b00667.

(46) Bianco, V.; Alonso-Navarro, M.; Di Silvio, D.; Moya, S.; Cortajarena, A. L.; Coluzza, I. Proteins Are Solitary! Pathways of Protein Folding and Aggregation in Protein Mixtures. J. Phys. Chem. Lett. 2019, 4800–4804. https://doi.org/10.1021/acs.jpclett.9b01753.

(47) Cardelli, C.; Nerattini, F.; Tubiana, L.; Bianco, V.; Dellago, C.; Sciortino, F.; Coluzza, I. General Methodology to Identify the Minimum Alphabet Size for Heteropolymer Design. Adv. Theory Simulations 2019, 2 (7), 1900031. https://doi.org/10.1002/adts.201900031.

(48) Nerattini, F.; Tubiana, L.; Cardelli, C.; Bianco, V.; Dellago, C.; Coluzza, I. Design of Protein–Protein Binding Sites Suggests a Rationale for Naturally Occurring Contact Areas. J. Chem. Theory Comput. 2019, 15 (2), 1383–1392. https://doi.org/10.1021/acs.jctc.8b00667.

(49) Nerattini, F.; Figliuzzi, M.; Cardelli, C.; Tubiana, L.; Bianco, V.; Dellago, C.; Coluzza, I. Identification of Protein Functional Regions. ChemPhysChem 2020, 21 (4), 335–347. https://doi.org/10.1002/cphc.201900898.

(50) Meesaragandla, B.; García, I.; Biedenweg, D.; Toro-Mendoza, J.; Coluzza, I.; Liz-Marzán, L. M.; Delcea, M. H-Bonding-Mediated Binding and Charge Reorganization of Proteins on Gold Nanoparticles. Phys. Chem. Chem. Phys. 2020, 22 (8), 4490–4500. https://doi.org/10.1039/c9cp06371d.

(51) Bianco, V.; Franzese, G.; Coluzza, I. In Silico Evidence That Protein Unfolding Is a Precursor of Protein Aggregation. ChemPhysChem 2020, cphc.201900904. https://doi.org/10.1002/cphc.201900904.