Publications of Cristian Micheletti

Publications are listed in reverse cronological order. Electronic versions of the reprints are available upon request (please write to michelet _at_ sissa.it).

• V. Panizza, P. Hauke, C. Micheletti and P. Faccioli
  Protein Design by Integrating Machine Learning and Quantum-encoded Optimization
  PRX Life 2 043012 (2024)
  Abstract Link to online article



• J. Luengo-Marquez, S. Assenza, and C. Micheletti
  Shape and size tunability of sheets of interlocked ring copolymers
  Soft Matter 20 6595-6607 (2024)
  Abstract Link to online article



• L. Tubiana et al.
  Topology in Soft and Biological Matter
  Physics Reports 1075 1-137 (2024)
  Abstract Link to online article Review Article
  




• M. Caraglio, C. Micheletti and E. Orlandini
  Unraveling the Influence of Topology and Spatial Confinement on Equilibrium and Relaxation Properties of Interlocked Ring Polymers
  Macromolecules 57 3223-3233 (2024)
  Abstract Link to online article



• A. Tagliabue, C. Micheletti and M. Mella
  Effect of Counterion Size on Knotted Polyelectrolyte Conformations
  J. Phys. Chem. B 128 4183-4194(2024)
  Abstract Link to online article



• C. Micheletti, I. Chubak, E. Orlandini and J. Smrek
  Topology-Based Detection and Tracking of Deadlocks Reveal Aging of Active Ring Melts
  ACS Macro Lett. 13 124-129 (2024)
  Abstract Link to online article



• F. Slongo, P. Hauke, P. Faccioli and C. Micheletti
  Quantum-inspired encoding enhances stochastic sampling of soft matter systems
  Science Adv. 9 art. no. eadi0204 (2023)
  Abstract, Link to online article



• Z. Ahmadian Dehaghani, P. Chiarantoni and C. Micheletti
  Topological Entanglement of Linear Catenanes: Knots and Threadings
  ACS Macro Lett., 12, 1231-1236 (2023)
  Abstract, Link to online article



• G. Lazzeri, C. Micheletti, S. Pasquali and P. Faccioli
  RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias
  Biophys. J., 122, 3089-3098 (2023)
  Abstract, Link to online article



• P. Chiarantoni and C. Micheletti
  Linear catenanes in channel confinement
  Macromolecules, 56, 2736 (2023)
  Abstract, Link to online article



• V. Sorichetti, A. Ninarello, J.M. Ruiz Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob and L. Rovigatti
  Structure and elasticity of model disordered, polydisperse and defect-free polymer networks
  J. Chem. Phys, 158, 074905 (2023)
  Abstract, Link to online article Cover article



• A. Suma, V. Carnevale and C. Micheletti
  Nonequilibrium thermodynamics of DNA nanopore unzipping
  Phys. Rev. Lett., 130, 048101 (2023)
  Abstract, Link to online article



• S.-J. Chen et al.
  Opinion: Protein folds vs. protein folding: Differing questions, different challenges
  Proc. Natl. Acad. Sci. USA, 120, e2214423119 (2023)
  Abstract, Link to online article Opinion Article
  




• A. Tagliabue, C. Micheletti and M. Mella
  Tuning Knotted Copolyelectrolyte Conformations via Solution Properties
  Macromolecules, 55, 10761-10772 (2022)
  Abstract, Link to online article



• M. Becchi, R. Capelli, C. Perego, G.M. Pavan and C. Micheletti
  Density-tunable pathway complexity in a minimalistic self-assembly model
  Soft Matter, 18, 8106-8116 (2022)
  Abstract, Link to online article



• P. Chiarantoni and C. Micheletti
  Effect of ring rigidity on the statics and dynamics of linear catenanes
  Macromolecules, 55, 4523-4532 (2022)
  Abstract, Link to online article



• G. Amici, M. Caraglio, E. Orlandini and C. Micheletti
  Topological Friction and Relaxation Dynamics of Spatially Confined Catenated Polymers
  ACS Macro Lett., 11, 1-6 (2022)
  Abstract, Link to online article



• E. Orlandini and C. Micheletti
  Topological and Physical Links in Soft Matter Systems
  J. Phys. Condensed Matter, 34, 013002 (2022)
  Abstract, Link to online article Review Article
  




• A. Tagliabue, C. Micheletti and M. Mella
  Tunable knot segregation in co-polyelectrolyte rings carrying a neutral segment
  ACS Macro Letters, 10, 1365-1370 (2021)
  Abstract, Link to online article



• C. Micheletti, P. Hauke, P. Faccioli
  Polymer Physics by Quantum Computing
  Phys. Rev. Lett., 127, 080501 (2021)
  Abstract, Link to online article Link to Physics World highlight


• Hewafonsekage Y.Y. Fonseka, A. Javidi, L.F.L. Oliveira, C. Micheletti, and G. Stan
  Unfolding and Translocation of Knotted Proteins by Clp Biological Nanomachines: Synergistic Contribution of Primary Sequence and Topology Revealed by Molecular Dynamics Simulations
  J. Phys. Chem. B, 125, 7335-7350 (2021)
  Abstract, Link to online article Cover article



• S. Franzini, M. Di Stefano and C. Micheletti
  essHi-C: essential component analysis of Hi-C matrices
  Bioinformatics, 37, 2088-2094 (2021)
  Abstract, Link to online article



• M. Becchi, P. Chiarantoni and C. Micheletti
  RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration
  J. Phys. Chem. B, 125, 1098-1196 (2021)
  Abstract, Link to online article



• A. Suma, L. Coronel, G. Bussi and C. Micheletti
  Directional translocation resistance of Zika xrRNA
  Nature Communications, 11, art no. 3749 (2020)
  Abstract, Link to online article



• D. Michieletto, E. Orlandini, M.S. Turner and C. Micheletti
  Separation of Geometrical and Topological entanglement in Confined polymers Driven out of Equilibrium
  ACS Macro Letters, 9, 1081-1085 (2020)
  Abstract, Link to online article



• D. Agostinelli, R. Cerbino, J.C. Del Alamo, A. De Simone, S. Hohn, C. Micheletti, G. Noselli, E. Sharon and J. Yeomans
  MicroMotility: State of the art, recent accomplishments and perspectives on the mathematical modeling of bio-motility at microscopic scales
  Mathematics in Engineering, 2, 230-252 (2020)
  Abstract, Link to online article



• A. Rosa, M. Di Stefano and C. Micheletti
  Topological Constraints in Eukaryotic Genomes and How They Can Be Exploited to Improve Spatial Models of Chromosomes
  Front. Mol. Biosci., 6, 127 (2019)
  Abstract, Link to online article Opinion article



• A. Suma, E. Poppleton, M. Matthies, P. Sulc, F. Romano, A.A. Louis, J.P.K. Doye, C. Micheletti and L. Rovigatti
  TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami
  J. Comput. Chem., 40, 2586-2595 (2019)
  Abstract, Link to online article Cover article Link to cover



• A. Valdes, L. Coronel, B. Martinez-Garcia, J. Segura, S. Dyson, O. Diaz-Ingelmo, C. Micheletti and J. Roca
  Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA
  Nucleic Acids Res., 47, 6946-6955 (2019)
  Abstract, Link to online article



• L. Weiss, M. Marenda, C. Micheletti and C. Likos
  Hydrodynamics and Filtering of Knotted Ring Polymers in Nanochannels
  Macromolecules, 52 , p. 4111-4119 (2019)
  Abstract, Link to online article



• G. Amici, M. Caraglio, E. Orlandini and C. Micheletti
  Topologically Linked Chains in Confinement
  ACS Macro Lett., 8 , 442-446 (2019)
  Abstract, Link to online article



• E. Uehara, L. Coronel, C. Micheletti and T. Deguchi
  Bimodality in the knotting probability of semiflexible rings suggested by mapping with self-avoiding polygons
  Reactive and Functional Polymers, 134, 141-149 (2019)
  Abstract, Link to online article



• M. Marenda, E. Orlandini and C. Micheletti
  Discovering privileged topologies of molecular knots with self-assembling models
  Nature Communications, 9, 3051 (2018)
  Abstract, Link to online article
  Link to blog in Nature Chemistry Community
  Link to interactive Science News article by Emily Conover Link to Quanta Magazine article by Jordana Cepelewicz
  



• L. Coronel, A. Suma and C. Micheletti
  Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking
  Nucleic Acids Res., 46, 7533 (2018)
  Abstract, Link to online article Cover article for NAR issue of Sept. 6, 2018



• A. Suma, M. Di Stefano and C. Micheletti
  Electric-field-driven trapping of polyelectrolytes in needle-like backfolded states
  Macromolecules, 51, 4462-4470 (2018)
  Abstract, Link to online article



• L. Tubiana, G. Polles, E. Orlandini and C. Micheletti
  KymoKnot: a web-server and software package to identify and locate knots in trajectories of linear or circular polymers
  Eur. Phys. J., 41, 72 (2018)
  Abstract, Link to online article Link to Kymoknot webserver Cover article for EPJ E issue of June 6, 2018



• A.L. Bozic, C. Micheletti, R. Podgornik and L. Tubiana
  Compactness of viral genomes: effect of disperse and localized random mutations
  J. Phys. Condensed Matter, 30, 084006 (2018)
  Abstract, Link to online article



• M. Adorisio, A. Pezzotta, C. de Mulatier, C. Micheletti and A. Celani
  Exact and Efficient Sampling of Conditioned Walks
  J. Stat. Phys, 170 79-100 (2018)
  Abstract, Link to online article



• D. Granata, L. Ponzoni, C. Micheletti and V. Carnevale
  Patterns of coevolving amino acids unveil structural and dynamical domains
  Proc. Natl. Acad. Sci. USA, 114, E10612-E10621 (2017)
  Abstract, Link to online article



• M. Caraglio, C. Micheletti and E. Orlandini
  Mechanical pulling of linked ring polymers: elastic response and link localisation
  Polymers, 9, 327 (2017)
  Abstract, Link to online article



• C. Micheletti and H. Orland
  Efficient Sampling of Knotting-Unknotting Pathways for Semiflexible Gaussian Chains
  Polymers, 9, art. no. 196 (2017)
  Abstract, Link to online article



• L. Coronel, E. Orlandini and C. Micheletti
  Non-monotonic knotting probability and knot length of semiflexible rings: the competing roles of entropy and bending energy
  Soft Matter, 13, 4260-4267 (2017)
  Abstract, Link to online article



• M. Caraglio, C. Micheletti and E. Orlandini
  Physical links: defining and detecting inter-chain entanglement
  Scientific Reports, 7, art. no. 1156 (2017)
  Abstract, Link to online article



• A. Suma and C. Micheletti
  Pore translocation of knotted DNA rings
  Proc. Natl. Acad. Sci. USA, 114, E2991-E2997 (2017)
  Abstract, Link to online article



• E. Orlandini, G. Polles, D. Marenduzzo and C. Micheletti
  Self-assembly of knots and links
  J. Stat. , art no. 034003 (2017)
  Abstract, Link to online article



• A. Japaridze, E. Orlandini, K. Smith, L. Gmuer, F. Valle, C. Micheletti and G. Dietler
  Spatial confinement induces hairpins in nicked circular DNA
  Nucl. Acids Res., 45, 4905-4914 (2017)
  Abstract, Link to online article



• L. Ponzoni, G. Rossetti, L. Maggi, A. Giorgetti, P. Carloni and C. Micheletti
  Unifying view of mechanical and functional hotspots across class A GPCRs
  Plos. Comput. Biol., 13, art no. e1005381 (2017)
  Abstract, Link to online article



• G. D'Adamo, E. Orlandini and C. Micheletti
  Linking of ring polymers in slit-like confinement
  Macromolecules, 50, 1713-1718 (2017)
  Abstract, Link to online article



• M. Marenda, E. Orlandini and C. Micheletti
  Sorting ring polymers by knot type with modulated nanochannels
  Soft Matter, 13 , 795 (2017)
  Abstract, Link to online article



• S.E. Jackson, A. Suma and C. Micheletti
  How to fold intricately: using theory and experiments to unravel the properties of knotted proteins
  Curr. Op. Struct. Biol., 42, 6-14 (2017)
  Abstract, Link to online article



• M. Di Stefano J. Paulsen, T.G. Lienn E. Hovig and C. Micheletti
  Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization
  Scientific Reports, 2016, 6 , art. no 35985
  Abstract, Link to online article covered story by Elizabeth Pennisi in Science magazine, Nov. 1, 2016



• G. Polles, E. Orlandini and C. Micheletti
  Optimal Self-Assembly of Linked Constructs and Catenanes via Spatial Confinement
  ACS Macro Letters, 2016, 5 , 931-935
  Abstract, Link to online article



• G. D'Adamo, G. Dietler and C. Micheletti
  Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains
  Soft Matter, 2016,12 ,6708-6715
  Abstract, Link to online article Inside front cover for issue 2016/32 of Soft Matter



• A.S. Burton, M. Di Stefano, N. Lehman, H. Orland and C. Micheletti
  The elusive quest for RNA knots
  RNA Biology, 2016, 13 , 134-139
  Abstract, Link to online article (Open Access) Point of View article



• A. Suma, A. Rosa and C. Micheletti
  Pore translocation of knotted polymer chains: how friction depends on knot complexity
  ACS Macro Letters, 2015, 4 , 1420-1424
  Abstract, Link to online article



• M. Caraglio, C. Micheletti and E. Orlandini
  Stretching response of knotted and unknotted chains
  Phys. Rev. Lett., 2015, 115 , 188301
  Abstract, Link to online article



• G. D'Adamo and C. Micheletti
  Molecular crowding increases knots abundance in linear polymers
  Macromolecules, 2015, 48 , 6337
  Abstract, Link to online article



• G. Pinamonti, S. Bottaro, C. Micheletti and G. Bussi
  Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
  Nucl. Acids Res., 2015, 43 , 7260-7269
  Abstract, Link to online article



• L. Ponzoni, G. Polles, V. Carnevale and C. Micheletti
  SPECTRUS: a dimensionality reduction approach for identifying dynamical domains in protein complexes from limited structural datasets
  Structure, 2015, 23 , 1516-1525
  Abstract, Link to online article Cover article for the August 2015 issue of STRUCTURE



• G. D'Adamo, D. Marenduzzo, C. Micheletti, and E. Orlandini
  Electric field controlled columnar and planar patterning of cholesteric colloids
  Phys. Rev. Lett., 2015, 114 , art. no. 177801
  Abstract, Link to online article Cover article for the May 1 2015 issue of Phys Rev Lett.

  Selected for a Synopsis in Physics and an Editors' Suggestion.



• A. Suma, E. Orlandini and C. Micheletti
  Knotting dynamics of DNA chains of different length confined in nanochannels
  J. Phys. Condensed Matter, 2015, 27 , art no. 354102
  Abstract, Link to online article



• G. Polles, D. Marenduzzo, E. Orlandini and C. Micheletti
  Self-assembling knots of controlled topology by designing the geometry of patchy templates
  Nature Communications, 2015, 6 , art. no 6423
  Abstract, Link to online article Link to video demo of self-assembling knots out of 3D-printed templates.



• C. Micheletti, M. Di Stefano and H. Orland
  Absence of knots in known RNA structures
  Proc. Natl. Acad. Sci. USA, 2015, 112 , 2052-2057
  Abstract, Link to online article Link to article by Janelle Weaver in Biotechniques



• L. Tubiana, A.L. Bozic, C. Micheletti and R. Podgornik
  Synonymous mutations reduce genome compactness in icosahedral ssRNA viruses
  Biophysical Journal, 2015, 108 , 194-202
  Abstract, Link to online article Cover article for the January 6 2015 issue of Biophysical Journal.

  Link to accompanying "New and Notable" article by W. Gelbart and A. Ben-Shaul.



• F. Musiani, G. Rossetti, L. Capece, T. Gerger, C. Micheletti, G. Varani and P. Carloni
  MD simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 TAR RNA
  J. Am. Chem. Soc., 2014, 136 , 15631-15637
  Abstract, Link to online article



• C. Micheletti and E. Orlandini
  Knotting and unknotting dynamics of DNA strands in nanochannels
  ACS Macro Letters, 2014, 3 , 876-880
  Abstract, Link to online article



• M. Di Stefano, L. Tubiana, M. Di Ventra and C. Micheletti
  Driving knots on DNA with AC/DC electric fields: topological friction and memory effects
  Soft Matter, 2014, 10 , 6491-6498
  Abstract, Link to online article



• R. Covino, T. Skrbic, S. a Beccara, P. Faccioli and C. Micheletti
  The role of non-native interactions in the folding of knotted proteins: insights from molecular dynamics simulations
  Biomolecules, 2014, 4 , 1-19
  Abstract, Link to online article



• D. Marenduzzo, C. Micheletti, E. Orlandini and D.W. Sumners
  Topological friction strongly affects viral DNA ejection
  Proc. Natl. Acad. Sci. USA, 2013, 110 20081-20086-
  Abstract, Link to online article



• G. Polles, G. Indelicato, R. Potestio, P. Cermelli, R. Twarock, C. Micheletti
  Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition
  PLoS Comput. Biol., 2013, 9, e1003331
  Abstract, Link to online article Cover article for the November 2013 issue of PLoS Comput. Biol.



• F. Musiani, E. Ippoliti, C. Micheletti, P. Carloni and S. Ciurli
  Conformational fluctuations of UreG, an intrinsically disordered enzyme
  Biochemistry., 2013, 52 2949 - 2954
  Abstract, Link to online article



• L. Tubiana, A. Rosa, F. Fragiacomo and C. Micheletti
  Spontaneous knotting and unknotting of flexible linear polymers: equilibrium and kinetic aspects
  Macromol., 2013, 46 3669-3678
  Abstract, Link to online article Cover article for issue n. 11/2013 of the journal
  

Link to arXiv preprint ,




• D. Marenduzzo, C. Micheletti and E. Orlandini
  The knotted strands of life
  Physics World, April 2013, p. 30-34,
  Link to online article Feature article
  



• M. Di Stefano, A. Rosa, V. Belcastro, D. di Bernardo, C. Micheletti
  Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19
  PLoS Comput. Biol., 2013, 9, e1003019
  Link to online article Cover article for the March 2013 issue of PLoS Comput. Biol.
  

Abstract, Link to arXiv preprint




• S. a Beccara, T. Skrbic, R. Covino, C. Micheletti, P. Faccioli
  Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
  PLoS Comput. Biol., 2013, 9 , e1003002
  Link to online article , Abstract,



• E. Orlandini and C. Micheletti
  Knotting of linear DNA in nano-slits and nano-channels: a numerical study
  Journal of Biological Physics, 2013, 39 , 267-275
  Abstract, Link to arXiv preprint , Link to online article



• C. Micheletti
  Comparing proteins by their internal dynamics: Exploring structure-function relationships beyond static structural alignments
  Physics of Life Reviews, 2013, 10 , 1-26
  Abstract, Link to online article Review Article followed by 6 commentaries by: P.K. Agarwal, P.C. Biggins, J. Echave, R.L. Jernigan, A.M. Lesk, M. Orozco
  

Link to arXiv preprint ,




• M. Bon, C. Micheletti and H. Orland
  McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots
  Nucl. Acids Res., 2013, 41 , 1895-1900
  Abstract, Link to online article , Link to arXiv preprint ,



• A. Rosa, M. Di Ventra and C. Micheletti
  Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore
  Phys. Rev. Lett, 2012, 109 , 118301
  Abstract, Link to online article



• C. Micheletti and E. Orlandini
  Knotting and metric scaling properties of DNA confined in nano-channels: a Monte Carlo study
  Soft Matter, 2012, 8 , 10959-10968
  Abstract, Link to online article Highlighted by RSC as hot paper for February 2013



• T. Skrbic, C. Micheletti and P. Faccioli
  The Role of Non-native Interactions in the Folding of Knotted Proteins
  Plos. Comput. Biol., 2012, 8 , e1002504
  Abstract, Link to online article



• G. Morra, R. Potestio, C. Micheletti and G. Colombo
  Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations
  Plos. Comput. Biol., 2012 8 e1002433
  Abstract, Link to online article



• C. Micheletti and E. Orlandini
  Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties
  Macromolecules, 2012, 45 , 2113-2121
  Abstract, Link to arXiv preprint , Link to online article



• A. Bosco, F. Bano, P. Parisse, L. Casalis, A. DeSimone and C. Micheletti
  Hybridization in Nanostructured DNA Monolayers Probed by AFM: Theory Versus Experiment
  Nanoscale, 2012, 4 , 1734-1741
  Abstract, Link to online article



• A. Rosa, E. Orlandini, L. Tubiana and C. Micheletti
  Structure and dynamics of ring polymers: entanglement effects because of solution density and ring topology
  Macromolecules, 2011, 44 , 8668-8680
  Abstract, Link to arXiv preprint , Link to online article



• L. Tubiana, E. Orlandini and C. Micheletti
  Multiscale entanglement in ring polymers under spherical confinement
  Phys. Rev. Lett., 2011, 107, 188302
  Abstract, Link to arXiv preprint , Link to online article ,
  Selected for the Virtual Journal of Biological Physics Research, Vol. 22, issue 9.
  



• F. Benedetti, C. Micheletti, G. Bussi, S. K. Sekatskii and G. Dietler
  Non-kinetic modeling of the mechanical unfolding of multimodular proteins: theory and experiments
  Biophys. J., 2011, 101, p. 1504-1512
  Abstract, Link to online article



• L. Tubiana, E. Orlandini and C. Micheletti
  Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes
  Prog. Theor. Phys., 2011, 191 , 192-204
  Abstract , Link to online article , Link to arXiv preprint



• C. Micheletti, D. Marenduzzo and E. Orlandini
  Polymers with spatial or topological constraints: theoretical and computational results
  Physics Reports, 2011, 504 , p. 1-73
  Abstract, Link to arXiv preprint , Link to online article Topical Review
  



• F. Musiani, B. Bertosa, A. Magistrato, B. Zambelli, P. Turano, V. Losasso, C. Micheletti, S. Ciurli and P. Carloni
  Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+
  J. Chem. Theory Comput., 2010, 6, 3503-3515
  Abstract, Link to online article



• V. Carnevale, C. Micheletti, F. Pontiggia and R. Potestio
  Bridging the Atomic and Coarse-Grained descriptions of Collective Motions in Proteins
  Chapter 7 (pages 159-178) in book: Multiscale Approaches to Protein Modeling, Springer Verlag, 2010, ISBN-10: 1441968881
  Abstract ,



• A. Zen, C. Micheletti, O. Keskin and R. Nussinov
  Comparing interfacial dynamics in protein-protein complexes: an elastic network approach
  BMC Struct. Biol., 2010, 10:26 doi:10.1186/1472-6807-10-26
  Abstract , Link to online article Highly accessed



• R. Potestio, C. Micheletti and H. Orland
  Knotted vs. Unknotted Proteins: Evidence of Knot-Promoting Loops
  PlOS Comput. Biol., 2010; 6: e1000864. doi:10.1371/journal.pcbi.1000864
  Abstract , Link to online article ,
  



• D. Marenduzzo, C. Micheletti and E. Orlandini
  Biopolymer organization upon confinement
  J. Phys. Condens. Matter 22, 283102 (2010)
  Abstract , Link to online article Topical Review
  



• R. Potestio, T. Aleksiev, F. Pontiggia, S. Cozzini and C. Micheletti
  ALADYN: a web server for aligning proteins by matching their large-scale motion
  Nucl. Acids Res., 2010; doi: 10.1093/nar/gkq293
  Abstract , Link to online article



• D. Marenduzzo, E. Orlandini, A. Stasiak, D.W. Sumners, L. Tubiana and C. Micheletti
  DNA-DNA interactions in bacteriophage capsids are responsible for the observed DNA knotting
  Proc. Natl. Acad. Sci. USA 106, 22269-22274 (2009)
  Abstract , Link to online article ,
  Selected for the Virtual Journal of Biological Physics Research, Vol. 19, issue 1.



• T. Aleksiev, R. Potestio, S. Cozzini and C. Micheletti
  PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
  Bioinformatics 25, 2743-2744 (2009)
  Abstract , Link to online article , Link to PiSQRD Server.
  



• C. Micheletti and H. Orland
  MISTRAL: a tool for energy-based multiple structural alignment of proteins
  Bioinformatics 25, 2663-2669 (2009)
  Abstract , Link to online article., Link to MISTRAL Server
  



• A. Zen, C. de Chiara, A. Pastore and C. Micheletti
  Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains
  Bioinformatics 25, 1876-1883 (2009)
  Abstract , Link to online article.
  



• R. Potestio, F. Pontiggia, and C. Micheletti
  Coarse-Grained Description of Protein Internal Dynamics: An Optimal Strategy for Decomposing Proteins in Rigid Subunits
  Biophys J. 96 4993-5002 (2009)
  Abstract , Link to online article.
  



• C. Micheletti, D. Marenduzzo, E. Orlandini and D.W. Sumners
  Knot spectrum of confined self-avoiding walks
  In Proceedings of the conference: Knots and soft-matter physics. Bussei-Kenkyu (Kyoto) 38-42 (2009)
  Abstract



• V. Carnevale, S. Raugei, M. neri, S. Pantano, C. Micheletti and P. Carloni
  Multi-scale modeling of HIV-1 proteins
  Journal of Molecular Structure: THEOCHEM 89897-105 (2009)
  Abstract , Link to online article.
  



• F. Pontiggia, A. Zen and C. Micheletti
  Small and large scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics
  Biophys J. 95 5901 (2008)
  Abstract , Link to online article.
  



• C. Micheletti, G. Bussi and A. Laio
  Optimal Langevin modelling of out-of-equilibrium molecular dynamics simulations
  J. Chem. Phys 129 074105 (2008)
  Abstract , Link to online article.
  Selected for the Virtual Journal of Biological Physics Research, Vol. 16, issue 5.
  



• C. Micheletti, D. Marenduzzo, E. Orlandini and D.W. Sumners
  Simulations of knotting in confined circular DNA
  Biophys. J. 95 3591 (2008)
  Abstract , Link to online article.
  



• A. Zen, V. Carnevale, A.M. Lesk and C. Micheletti
  Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families
  Prot. Sci. 17 918-929 (2008)
  Abstract , Link to online article.
  



• F. Capozzi, C. Luchinat, C. Micheletti and F. Pontiggia
  Essential dynamics of helices provide a functional classification of EF-hand proteins
  J. Proteome Res. 6 4245-4255 (2007)
  Abstract , Link to online article.
  



• V. Carnevale, S. Raugei, C. Micheletti and P. Carloni
  Large-scale motions and electrostatic properties of Furin and HIV-1 protease
  J. Phys. Chem A 111 12327-12332 (2007)
  Abstract , Link to online article.
  



• V. Carnevale, F. Pontiggia and C. Micheletti
  Structural and dynamical alignment of enzymes with partial structural similarity
  J. Phys. Condens. Matt. 19 285206 (2007)
  Abstract , Link to online article.
  



• F. Pontiggia, G. Colombo, C. Micheletti and H. Orland
  Anharmonicity and self-similarity of the free energy landscape of protein G
  Phys. Rev. Lett. 98, art. No. 048102 (2007)
  Abstract , Link to online article.
  Selected for the Virtual Journal of Biological Physics Research, Vol. 13, issue 3.
  



• N.M. Toan, D. Marenduzzo, P.R. Cook and C. Micheletti
  Depletion effects and loop formation in self-avoiding polymers
  Phys. Rev. Lett. 97, art. No. 178302 (2006)
  Abstract , Link to online article.
  



• V. Carnevale, S. Raugei, C. Micheletti and P. Carloni
  Convergent dynamics in the protease enzymatic superfamily
  J. Am. Chem. Soc. 128, 9766-9772 (2006)
  Abstract , Link to online article.
  



• T. Keef, C. Micheletti and R. Twarock
  Master equation approach to the asembly of viral capsids
  J. Theor. Biol. 242, 713-721 (2006)
  Abstract , Link to online article.
  



• D. Marenduzzo, C. Micheletti and P.R. Cook
  Entropy-driven genome organization
  Biophys. J. 90 3712-3721 (2006)
  Abstract , Link to online article.
  



• P. Raiteri, A. Laio, F.L. Gervasio, C. Micheletti and M. Parrinello
  Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics
  J. Phys. Chem. B 110 3533-3539 (2006)
  Abstract , Link to online article.
  



• N.M. Toan and C. Micheletti
  Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA
  J. Phys.: Condens. Matter 18 S269-S281 (2006)
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, D. Marenduzzo, E. Orlandini, D. W. Sumners
  Knotting of random ring polymers in confined spaces
  J. Chem. Phys. 124 064903 (2006)
  Abstract , Preprint full text (cond-mat archive) , Link to online article ,
  Selected for the Virtual Journal of Biological Physics Research, Vol. 11, issue 4.
  



• A. Laio and C. Micheletti
  Are structural biases at protein termini a signature of vectorial folding?
  Proteins 62 17-23 (2006)
  Abstract , Preprint full text (q-bio archive) , Link to online article.
  



• G. Colombo and C. Micheletti
  Protein folding simulations: combining coarse-grained models and all-atom molecular dynamics
  Theor. Chem. Acc.116 75-86 (2006)
  Abstract , Link to online article.
  
  



• D. Marenduzzo, C. Micheletti, H. Seyed-allaei, A. Trovato and A. Maritan
  Continuum model for polymers with finite thickness
  J. Phys. A. 38 L277-L283 (2005)
  Abstract , Preprint full text (cond-mat archive). Link to online article.
  



• N.M. Toan, D. Marenduzzo and C. Micheletti
  Inferring the diameter of a biopolymer from its stretching response
  Biophysical Journal 89 80-86 (2005)
  Abstract , Preprint full text (cond-mat archive). Link to online article.
  



• M. Cascella, C. Micheletti, U. Rothlisberger and P. Carloni
  Evolutionarily Conserved Functional Mechanics across Pepsin-like and Retroviral Aspartic Proteases fluctuations on enzymatic activity
  J. Am. Chem. Soc. 127 3734-3742 (2005)
  Abstract , Link to online article.
  
  



• M. Neri, M. Cascella and C. Micheletti
  Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase
  J. Phys. Condens. Matter 17 S1581-S1593 (2005)
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• G.M.S. De Mori, G. Colombo and C. Micheletti
  Study of the Villin Headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom Molecular Dynamics
  Proteins 58 459-471 (2005).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• I. Ali, D. Marenduzzo, C. Micheletti and J.M. Yeomans
  A coarse grained model for DNA and polymer packaging: statics and dynamics
  J. Theor. Med. 6 115-117 (2005).
  Abstract , Link to online article.
  



• G.M.S. De Mori, C. Micheletti and G. Colombo
  All-Atom Folding Simulations of the Villin Headpiece from Stochastically Selected Coarse-Grained Structures
  J. Phys. Chem. B 108 12267-12270 (2004).
  Abstract , Link to online article.
  
  

  
  

• C. Micheletti, A. Laio and M. Parrinello
  Reconstructing the Density of States by History-Dependent Metadynamics
  Phys. Rev. Lett. 92 170601 (2004).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, P. Carloni and A. Maritan
  Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models
  Proteins, 55, 635 (2004).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  The source code of the programme which implements the Beta-Gaussian model described in this article is freely available upon request.
  



• C. Micheletti, V. De Filippis, A. Maritan and F. Seno
  Elucidation of the Disulfide-Folding Pathway of Hirudin by a Topology-Based Approach
  Proteins, 53, 720-730 (2003).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• D. Marenduzzo and C. Micheletti
  Thermodynamics of DNA packaging inside a viral capsid: The role of DNA intrinsic thickness
  J. Mol. Biol., 330, 485-492 (2003).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti
  Prediction of folding rates and transition-state placement from native-state geometry
  Proteins, 51, 74-84 (2003).
  Abstract , Link to online article.
  



• J.R. Banavar, A. Maritan, C. Micheletti and A. Trovato
  Geometry and physics of proteins
  Proteins: Structure, Function and Genetics, 47,315-322 (2002).
  Abstract , Link to online article.
  



• G. Settanni, T.X. Hoang, C. Micheletti and A. Maritan
  Folding pathways of prion and doppel
  Biophysical Journal, 83,3533-3541 (2002).
  Abstract , Link to online article



• C. Micheletti, F. Cecconi, A. Flammini and A. Maritan
  Crucial stages of protein folding through a solvable model: Predicting target sites for enzyme-inhibiting drugs
  Protein Science, 11, 1878-1887 (2002).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, G. Lattanzi and A. Maritan
  Elastic properties of proteins: Insight on the folding process and evolutionary selection of native structures
  J. Mol. Biol. 321, 909-921 (2002).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, J. R. Banavar and A. Maritan
  Conformations of proteins in equilibrium
  Phys. Rev. Lett., 87, DOI:088102-1 (2001).
  Abstract , Full text (cond-mat archive) , Link to online article.
  Selected for the Virtual Journal of Biological Physics Research, Vol. 2, issue 9.
  



• A. Rossi C. Micheletti, F. Seno and A. Maritan,
  Self-consistent knowledge-based approach to protein design
  Biophysical Journal, 80, 480-490 (2001).
  Abstract , Full text (cond-mat archive) , Link to online article.
  



• F. Cecconi, C. Micheletti, P. Carloni and A. Maritan,
  Molecular dynamics studies on HIV-1 protease: Drug resistance and folding pathways
  , Proteins, 43, 365-372 (2001).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, F. Seno, J. R. Banavar and A. Maritan
  Learning effective amino acid interactions through iterative stochastic techniques
  Proteins 42, 422-431 (2001).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  Supplementary material available.
  



• G. Giugliarelli, C. Micheletti, J. R. Banavar amd A. Maritan
  Compactness, aggregation, and prionlike behavior of protein: A lattice model study
  J. Chem. Phys., 113, 5072-5077 (2000)
  Abstract , Link to online article.
  Selected for the Virtual Journal of Biological Physics Research, Vol. 1, issue 9.



• A. Maritan, C. Micheletti, A. Trovato and J. R. Banavar,
  Optimal shapes of compact strings
  Nature, 406 287-290 (2000).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, F. Seno and A. Maritan
  Recurrent oligomers in proteins - an optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies.
  Proteins: Structure, Function and Genetics 40, 662-674, (2000).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  Supplementary material available.
  



• A. Maritan, C. Micheletti, and J. R. Banavar
  Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle.
  Phys. Rev. Lett., 84, 3009-3012 (2000)
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  Selected for the Virtual Journal of Biological Physics Research, Vol. 1, issue 4.
  



• R. Dima, G. Settanni, C. Micheletti, J. R. Banavar and A. Maritan
  Extraction of interaction potentials between amino acids from native protein structures
  J. Chem. Phys., 112, 9151-9166 (2000)
  Abstract , Link to online article ,
  Selected for the Virtual Journal of Biological Physics Research, Vol. 1, issue 5.



• A. Rossi, A. Maritan and C. Micheletti
  A Novel Iterative Strategy for Protein Design.
  J. Chem. Phys., 112, 2050-2055 (2000)
  Abstract , Preprint full text (cond-mat archive) , Link to online article ,
  Selected for the Virtual Journal of Biological Physics Research, Vol. 1, issue 2.
  



• C. Micheletti, F. Seno, A. Maritan and J. R. Banavar,
  Strategies for protein folding and design.
  Ann. Comb. 3, 431-450 (1999).
  Abstract , Link to online article.
  



• J.P. Goff, R.S. Sarthour, C. Micheletti, S. Langringe, C. J. T. Wilkins, R. C. C. Ward and M. R. Wells.,
  Surface magnetic phase transitions in Dy/Lu superlattices
  J. Magnetism and magnetic materials, 199, 309-311 (1999). Link to online article.
  



• C. Micheletti, R. B. Griffiths and J. M. Yeomans,
  Surface spin-flop and discummensuration transitions in antiferromagnets.
  Phys. Rev. B 59, 6239-6249, (1999).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, J. R. Banavar, A. Maritan and F. Seno,
  Protein structures and optimal folding from a geometrical variational principle.
  Phys. Rev. Lett. 82, 3372-3375, (1999).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, A. Maritan and J. R. Banavar,
  A comparative study of existing and new design techniques for protein models
  J. Chem. Phys. 110, 9730-9738 (1999).
  Abstract , Preprint full text (cond-mat archive) Link to online article.
  



• F. Seno, C. Micheletti, A. Maritan, J. R. Banavar
  Variational approach to protein design and extraction of interaction potentials
  Phys. Rev. Lett. 81, 2172-2175 (1998)
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, J. R. Banavar, F. Seno and A. Maritan
  Steric constraints in model proteins
  Phys. Rev. Lett. 80, 5683-5686, (1998).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, F. Seno, A. Maritan and J. R. Banavar
  Design of proteins with hydrophobic and polar amino acids
  Proteins: Structure, Function and Genetics 32, 80-87, (1998).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, F. Seno, A. Maritan and J. R. Banavar,
  Protein Design in a Lattice Model of Hydrophobic and Polar Amino Acids
  Phys. Rev. Lett. 80, p. 2237-2240 (1998).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, A. B. Harris and J. M. Yeomans,
  Complete devil's staircase in the Falicov-Kimball model
  J. Phys A 30, L711-L717 (1997).
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, R. B. Griffiths and J. M. Yeomans,
  Surface spin-flop phases and bulk discommensurations in antiferromagnets
  J. Phys. A 30, L233-L238 (1997)
  Abstract , Preprint full text (cond-mat archive) , Link to online article.
  



• A. B. Harris, C. Micheletti and J. M. Yeomans,
  Complete Wetting in the Three-Dimensional Transverse Ising Model
  J. Stat. Phys. 84, 323-335 (1996).
  Preprint full text (cond-mat archive) , Link to online article.
  



• A. B. Harris, C. Micheletti and J. M. Yeomans,
  Lifting of Multiphase Degeneracy by Quantum Fluctuations
  Phys. Rev. B 52, 6684-6705 (1995).
  Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti, F. Seno and J. M. Yeomans,
  Upsilon point in a Spin Model
  Phys. Rev. B 52, 4353-4359 (1995).
  Preprint full text (cond-mat archive) , Link to online article.
  



• A.B. Harris, C. Micheletti and J. M. Yeomans,
  Quantum Fluctuations in the axial next-nearest-neighbor (ANNNI) Ising Model
  Phys. Rev. Lett. 74, 3045-3048 (1995).
  Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti and J. M. Yeomans,
  The role of spin anisotropy in the unbinding of interfaces
  Europhys. Lett. 28, 465-469 (1994).
  Preprint full text (cond-mat archive) , Link to online article.
  



• C. Micheletti and J. M. Yeomans,
  Exact Solution for the Adsorption transition of Row-Convex Polygons in the limit of zero Area-Fugacity
  Europhys. Lett 25, 1-4 (1994).
  Link to online article.
  



• C. Micheletti and J. M. Yeomans,
  Adsorption transition of directed vesicles in two dimensions
  J. Phys A 26, 5705-5712 (1993).
  Link to online article.
  





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• C. Micheletti, PhD Thesis, Oxford University (1996).
  Supervisor: Dr. Julia M. Yeomans.
  Thesis Title: Models with competing interactions.
  Full text in PDF format (830 Kb).
  

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