Physics and Chemistry of Biological Systems
Recent publications of PhD students
access_time October 22 2017

2017

  • Computational design of cyclic peptides for the customized oriented immobilization of globular proteins
    Soler M., Rodriguez A., Russo A., Adedeji A., Foumthuim C., Cantarutti C., Ambrosetti E., Casalis L., Corazza A., Scoles G., Marasco D., Laio A., Fortuna S.
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 19 (4) pp. 2740-2748 (2017)
    doi: 10.1039/c6cp07807a
  • Unraveling Mg2+-RNA binding with atomistic molecular dynamics
    Cunha R., Bussi G.
    RNA , 23 (5) pp. 628-638 (2017)
    doi: 10.1261/rna.060079.116
  • Pore translocation of knotted DNA rings
    Suma A., Micheletti C.
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 114 (15) (2017)
    doi: 10.1073/pnas.1701321114
  • Feasibility and coexistence of large ecological communities
    Grilli J., Adorisio M., Suweis S., Barabas G., Banavar J., Allesina S., Maritan A.
    NATURE COMMUNICATIONS , 8 (2017)
    doi: 10.1038/ncomms14389
  • How to fold intricately: using theory and experiments to unravel the properties of knotted proteins
    Jackson S., Suma A., Micheletti C.
    CURRENT OPINION IN STRUCTURAL BIOLOGY , 42 pp. 6-14 (2017)
    doi: 10.1016/j.sbi.2016.10.002
  • Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models
    Pinamonti G., Zhao J., Condon D., Paul F., Noe F., Turner D., Bussi G.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 13 (2) pp. 926-934 (2017)
    doi: 10.1021/acs.jctc.6b00982
  • From conformational spread to allosteric and cooperative models of E. coli flagellar motor
    Pezzotta A., Adorisio M., Celani A.
    JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT , (2017)
    doi: 10.1088/1742-5468/aa569e
  • Unifying view of mechanical and functional hotspots across class A GPCRs
    Ponzoni L., Rossetti G., Maggi L., Giorgetti A., Carloni P., Micheletti C.
    PLOS COMPUTATIONAL BIOLOGY , 13 (2) (2017)
    doi: 10.1371/journal.pcbi.1005381
  • Sorting ring polymers by knot type with modulated nanochannels
    Marenda M., Orlandini E., Micheletti C.
    SOFT MATTER , 13 (4) pp. 795-802 (2017)
    doi: 10.1039/c6sm02551j
  • Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations
    Casalino L., Palermo G., Abdurakhmonova N., Rothlisberger U., Magistrato A.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 13 (1) pp. 340-352 (2017)
    doi: 10.1021/acs.jctc.6b00905

2016

  • Modeling quorum sensing trade-offs between bacterial cell density and system extension from open boundaries
    Marenda M., Zanardo M., Trovato A., Seno F., Squartini A.
    SCIENTIFIC REPORTS Volume: 6 2016
  • Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement
    Cesari A., Gil-Ley A., Bussi G.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 12 Issue: 12 Pages 6192-6200 2016
  • Structural, dynamical and catalytic interplay between Mg2+ ions and RNA. Vices and virtues of atomistic simulations
    Casalino L., Magistrato A.
    INORGANICA CHIMICA ACTA Volume: 452 Pages 73-81 2016
  • Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses
    Sarti E., Gladich I., Zamuner S., Correia B., Laio A.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Volume: 84 Issue: 9 Pages 1312-1320 2016
  • Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns
    Casalino L., Palermo G., Rothlisberger U., Magistrato A.
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Volume: 138 Issue: 33 Pages 10374-10377 2016
  • Optimal Self-Assembly of Linked Constructs and Catenanes via Spatial Confinement
    Polles G., Odandini E., Micheletti C.
    ACS MACRO LETTERS Volume: 5 Issue: 8 Pages 931-935 2016
  • RNA folding pathways in stop motion
    Bottaro S., Gil-Ley A., Bussi G.
    NUCLEIC ACIDS RESEARCH Volume: 44 Issue: 12 Pages 5883-5891 2016
  • Non-Markovian effects on protein sequence evolution due to site dependent substitution rates
    Rizzato F., Rodriguez A., Laio A.
    BMC BIOINFORMATICS Volume: 17 2016
  • Empirical Corrections to the Amber RNA Force Field with Target Metadynamics
    Gil-Ley A., Bottaro S., Bussi G.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 12 Issue: 6 Pages 2790-2798 2016
  • Tracer motion in an active dumbbell fluid
    Suma A., Cugliandolo L., Gonnella G.
    JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT 2016
  • Density effects in entangled solutions of linear and ring polymers
    Nahali N., Rosa A.
    JOURNAL OF PHYSICS-CONDENSED MATTER Volume: 28 Issue: 6 2016

2015

  • Pore Translocation of Knotted Polymer Chains: How Friction Depends on Knot Complexity
    Suma A., Rosa A., Micheletti C.
    ACS MACRO LETTERS Volume: 4 Issue: 12 Pages 1420-1424 2015
  • Fluctuations of rotational and translational degrees of freedom in an interacting active dumbbell system
    Cugliandolo L., Gonnella G., Suma A.
    CHAOS SOLITONS & FRACTALS Volume: 81 Pages 556-566 2015
  • ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.
    Perez-Villa A., Darvas M., Bussi G.
    NUCLEIC ACIDS RESEARCH Volume: 43 Issue: 18 Pages 8725-34 2015
  • Knotting dynamics of DNA chains of different length confined in nanochannels.
    Suma A., Orlandini E., Micheletti C.
    JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL Volume: 27 Issue: 35 Pages 354102-354102 2015
  • Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
    Pinamonti G., Bottaro S., Micheletti C., Bussi G.
    NUCLEIC ACIDS RESEARCH Volume: 43 Issue: 15 Pages 7260-7269 2015
  • SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets
    Ponzoni L., Polles G., Carnevale V., Micheletti C.
    STRUCTURE Volume: 23 Issue: 8 Pages 1516-1525 2015
  • Motility-induced phase separation and coarsening in active matter
    Gonnella G., Marenduzzo D., Suma A., Tiribocchi A.
    COMPTES RENDUS PHYSIQUE Volume: 16 Issue: 3 Pages 316-331 2015
  • Rotational and translational diffusion in an interacting active dumbbell system
    Cugliandolo L. F., Gonnella G., Suma A.
    PHYSICAL REVIEW E Volume: 91 Issue: 6 2015
  • Native fold and docking pose discrimination by the same residue-based scoring function
    Sarti E., Granata D., Seno F., Trovato A., Laio A.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS Volume: 83 Issue: 4 Pages 621-630 2015
  • Self-assembling knots of controlled topology by designing the geometry of patchy templates
    Polles G., Marenduzzo D., Orlandini E., Micheletti C.
    NATURE COMMUNICATIONS Volume: 6 2015
  • Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
    Gil-Ley A., Bussi G.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 11 Issue: 3 Pages 1077-1085 2015
  • Absence of knots in known RNA structures
    Micheletti C., Di Stefano M., Orland H.
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 112 Issue: 7 Pages 2052-2057 2015
  • Using reweighted pulling simulations to characterize conformational changes in riboswitches.
    Di Palma F., Colizzi F., Bussi G.
    METHODS IN ENZYMOLOGY Volume: 553 Pages 139-62 2015
  • Accurate Multiple Time Step in Biased Molecular Simulations
    Ferrarotti M. J., Bottaro S., Perez-Villa A., Bussi G.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 11 Issue: 1 Pages 139-146 2015

2014

  • Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT
    Bisha I., Rodriguez A., Laio A., Magistrato A.
    PLOS COMPUTATIONAL BIOLOGY Volume: 10 Issue: 12 2014
  • The role of nucleobase interactions in RNA structure and dynamics
    Bottaro S., Di Palma F., Bussi G.
    NUCLEIC ACIDS RESEARCH Volume: 42 Issue: 21 Pages 13306-13314 2014
  • Dynamics of a homogeneous active dumbbell system
    Suma A., Gonnella G., Laghezza G., Lamura A., Mossa A., Cugliandolo L. F.
    PHYSICAL REVIEW E Volume: 90 Issue: 5 2014
  • Ru[(bpy)(2)(dppz)](2+) and Rh[(bpy)(2)(chrysi)](3+) Targeting Double Strand DNA: The Shape of the Intercalating Ligand Tunes the Free Energy Landscape of Deintercalation
    Franco D., Vargiu A. V., Magistrato A.
    INORGANIC CHEMISTRY Volume: 53 Issue: 15 Pages 7999-8008 2014
  • Role of Magnesium Ions and Ligand Stacking in the Adenine Riboswitch Folding
    Di Palma F., Colizzi F., Bussi G.
    BIOPHYSICAL JOURNAL Volume: 106 Issue: 2 2014
  • Sodium-Galactose Transporter: The First Steps of the Transport Mechanism Investigated by Molecular Dynamics
    Bisha I., Rodriguez A., Sgrignani J., Magistrato A., Laio A.
    BIOPHYSICAL JOURNAL Volume: 106 Issue: 2 2014
  • Mechanism of Ionic Permeation in the Mimics of CNG Channels: A Structural, Functional and Computational Analysis
    Napolitano L. M. R., Bisha I., Arcangeletti M., Marchesi A., De March M., Onesti S., Laio A., Torre V.
    BIOPHYSICAL JOURNAL Volume: 106 Issue: 2 2014
  • Driving knots on DNA with AC/DC electric fields: topological friction and memory effects
    Di Stefano M., Tubiana L., Di Ventra M., Micheletti C.
    SOFT MATTER Volume: 10 Issue: 34 Pages 6491-6498 2014

2013

  • BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures
    Sarti E., Zamuner S., Cossio P., Laio A., Seno F., Trovato A.
    COMPUTER PHYSICS COMMUNICATIONS Volume: 184 Issue: 12 Pages 2860-2865 2013
  • Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
    Polles G., Indelicato G., Potestio R., Cermelli P., Twarock R., Micheletti C.
    PLOS COMPUTATIONAL BIOLOGY Volume: 9 Issue: 11 2013
  • Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
    Di Palma F., Colizzi F., Bussi G.
    RNA-A PUBLICATION OF THE RNA SOCIETY Volume: 19 Issue: 11 Pages 1517-1524 2013
  • Sodium-Galactose Transporter: first steps of transport mechanism investigated by molecular dynamics
    Bisha I., Laio A., Magistrato A., Giorgetti A., Sgrignani J.
    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 42 2013
  • Development of Electrochemical Impedance Immunosensors as Point of Care Medical Diagnostic Tools
    Ianeselli L., Grenci G., Tormen M., Casalis L., Laio A.
    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 42 2013
  • Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations
    Franco D., Sgrignani J., Bussi G., Magistrato A.
    JOURNAL OF CHEMICAL INFORMATION AND MODELING Volume: 53 Issue: 6 Pages 1371-1387 2013
  • Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics
    Granata D., Camilloni C., Vendruscolo M., Laio A.
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 110 Issue: 17 Pages 6817-6822 2013
  • Conformational transitions in adenine sensing riboswitch: A computational study
    Di Palma F., Colizzi F., Bussi G.
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY Volume: 245 2013
  • Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19
    Di Stefano M., Rosa A., Belcastro V., di Bernardo D., Micheletti C.
    PLOS COMPUTATIONAL BIOLOGY Volume: 9 Issue: 3 2013
  • The 3.5 angstrom X-ray structure of the human connexin26 gap junction channel is unlikely that of a fully open channel
    Zonta F., Polles G., Sanasi M. F., Bortolozzi M., Mammano F.
    CELL COMMUNICATION AND SIGNALING Volume: 11 2013
  • A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations
    Bisha I., Laio A., Magistrato A., Giorgetti A., Sgrignani J.
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 9 Issue: 2 Pages 1240-1246 2013
  • Thermodynamics of an Intrinsically Disordered Protein by Atomistic Simulations
    Granata D., Baghal F. B., Camilloni C., Vendruscolo M., Laio A.
    BIOPHYSICAL JOURNAL Volume: 104 Issue: 2 2013

2012

  • Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail
    Baftizadeh, Fahimeh; Biarnes, Xevi; Pietrucci, Fabio; Affinito, Fabio; Laio, Alessandro
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Volume: 134 Issue: 8 Pages: 3886-3894 2012
  • Hybridization in nanostructured DNA monolayers probed by AFM: theory versus experiment
    Bosco, Alessandro; Bano, Fouzia; Parisse, Pietro; Casalis, Loredana; DeSimone, Antonio; Micheletti, Cristian
    NANOSCALE Volume: 4 Issue: 5 Pages: 1734-1741 2012
  • The role of stochasticity in a model of retinal angiogenesis
    Capasso, Vincenzo; Morale, Daniela; Facchetti, Giuseppe
    IMA JOURNAL OF APPLIED MATHEMATICS Volume: 77 Issue: 6 Pages: 729-747 2012
  • A small chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: Structure-based design, synthesis, and biological evaluation
    Chiriano, Gianpaolo; De Simone, Angela; Mancini, Francesca; Perez, Daniel I.; Cavalli, Andrea; Bolognesi, Maria Laura; Legname, Giuseppe; Martinez, Ana; Andrisano, Vincenza; Carloni, Paolo; Roberti, Marinella
    EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY Volume: 48 Issue: -- Pages: 206-213 2012
  • A simple and efficient statistical potential for scoring ensembles of protein structures
    Cossio, Pilar; Granata, Daniele; Laio, Alessandro; Seno, Flavio; Trovato, Antonio
    SCIENTIFIC REPORTS Volume: 2 Issue: -- Pages: --- 2012
  • Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA
    Do, Trang N.; Ippoliti, Emiliano; Carloni, Paolo; Varani, Gabriele; Parrinello, Michele
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 8 Issue: 2 Pages: 688-694 2012
  • Exploring the low-energy landscape of large-scale signed social networks
    Facchetti, G.; Iacono, G.; Altafini, C.
    PHYSICAL REVIEW E Volume: 86 Issue: 3 Pages: --- 2012
  • Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer
    Facchetti, G.; Zampieri, M; Altafini, C.
    BMC Systems Biology Volume: 6 Issue: 1 Pages: 115 2012
  • A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations
    Ghaemi, Zhaleh; Minozzi, Manuela; Carloni, Paolo; Laio, Alessandro
    JOURNAL OF PHYSICAL CHEMISTRY B Volume: 116 Issue: 29 Pages: 8714-8721 2012
  • Interactions of iron-sulfur clusters with small peptides: insights into early evolution
    Hong Enriquez, Rolando P; Do, Trang N
    Computational biology and chemistry Volume: 41 Issue: -- Pages: 58-61 2012

2011

  • Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?
    Cossio, P.; Laio, A.; Pietrucci, F.
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS Volume: 13 Issue: 48 Pages: 21648-21649 2011
  • Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations
    Rossetti, G.; Cossio, P.; Laio, A.; Carloni, P.
    FEBS LETTERS Volume: 19 Pages: 3086-3089 2011
  • Probing the Entanglement and Locating Knots in Ring Polymers: A Comparative Study of Different Arc Closure Schemes
    Tubiana, L.; Orlandini, E.; Micheletti, C.
    PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT Issue: 91 2011
  • Multiscale Entanglement in Ring Polymers under Spherical Confinement
    Tubiana, L.; Orlandini, E.; Micheletti, C.
    PHYSICAL REVIEW LETTERS Volume: 107 Issue: 18 Page: 188302 2011
  • Structure and Dynamics of Ring Polymers: Entanglement Effects Because of Solution Density and Ring Topology
    Rosa, A.; Orlandini, E.; Tubiana, L.; Micheletti, C.
    MACROMOLECULES Volume: 44 Issue: 21 Pages: 8668-8680 2011
  • Theoretical Studies of Homogeneous Catalysts Mimicking Nitrogenase
    Sgrignani, J.; Franco, D.; Magistrato, A.
    MOLECULES Volume: 16 Issue: 1 Pages: 442-465 2011
  • Computing global structural balance in large-scale signed social networks
    Facchetti, Giuseppe; Iacono, Giovanni; Altafini, Claudio
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volume: 108 Issue: 52 Pages: 20953-20958 2011
  • Synthesis of Monomeric Derivatives To Probe Memoquin's Bivalent Interactions
    Bolognesi, M.; Chiriano, G.; Bartolini, M.; Mancini, F.; Bottegoni, G Maestri, V.; Czvitkovich, S.; Windisch, M.; Cavalli, A.; Minarini, A.; Rosini, M.; Tumiatti, V.; Andrisano, V.; Melchiorre, C.
    JOURNAL OF MEDICINAL CHEMISTRY Volume: 54 Issue: 24 Pages: 8299-8304 2011
  • Shaping substrates at the nanoscale for single cell characterization
    Corvaglia, S.; Ianeselli, L.; Cesselli, D.; Beltrami, A.; Scoles, G.; Scaini, D.; Casalis, L.
    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 40 Page: 226 2011
  • Selective bio-functionalization of electrodes inside micro and nano fluidic channels
    Ianeselli, L.; Casalis, L.; Silvestrini, M.; Grenci, G.; Tormen, M.; Scoles, G.
    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS Volume: 40 Page: 228 2011
  • Hybrid Lipoic Acid Derivatives to Attack Prion Disease on Multiple Fronts
    Bongarzone, S.; Tran, H.N.A.; Cavalli, A.; Roberti, M.; Rosini, M.; Carloni, P.; Legname, G.; Bolognesi, M.L.
    CHEMMEDCHEM Volume: 6 Issue: 4 Page: 601-605 2011
  • Sequential Virtual Screening Approach to the Identification of Small Organic Molecules as Potential BACE-1 Inhibitors
    Chiriano, G.; Sartini, A.; Mancini, F.; Andrisano, V.; Bolognesi, M.L.; Roberti, M.; Recanatini, M.; Carloni, P.; Cavalli, A.
    CHEMICAL BIOLOGY & DRUG DESIGN Volume: 77 Issue: 4 Pages: 268-271 2011
  • The concept of privileged structures in rational drug design: focus on acridine and quinoline scaffolds in neurodegenerative and protozoan diseases
    Bongarzone, Salvatore; Bolognesi, Maria Laura
    EXPERT OPINION ON DRUG DISCOVERY Volume: 6 Issue: 3 Pages: 251-268 2011