Physics and Chemistry of Biological Systems
Publications of the group
access_time October 22 2017

2017

  • Bellucci L., Bussi G., Di Felice R., Corni S.
    Fibrillation-prone conformations of the amyloid-beta-42 peptide at the gold/water interface
    NANOSCALE , 9 (6) pp. 2279-2290 (2017)
    doi: 10.1039/c6nr06010b
  • 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.
    Computational design of cyclic peptides for the customized oriented immobilization of globular proteins
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 19 (4) pp. 2740-2748 (2017)
    doi: 10.1039/c6cp07807a
  • Giorgino T., Laio A., Rodriguez A.
    METAGUI 3: A graphical user interface for choosing the collective variables in molecular dynamics simulations
    COMPUTER PHYSICS COMMUNICATIONS , 217 pp. 204-209 (2017)
    doi: 10.1016/j.cpc.2017.04.009
  • Japaridze A., Orlandini E., Smith K., Gmur L., Valle F., Micheletti C., Dietler G.
    Spatial confinement induces hairpins in nicked circular DNA
    NUCLEIC ACIDS RESEARCH , 45 (8) pp. 4905-4914 (2017)
    doi: 10.1093/nar/gkx098
  • Magistrato A., Sgrignani J., Krause R., Cavalli A.
    Single or Multiple Access Channels to the CYP450s Active Site? An Answer from Free Energy Simulations of the Human Aromatase Enzyme
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS , 8 (9) pp. 2036-2042 (2017)
    doi: 10.1021/acs.jpclett.7b00697
  • Cunha R., Bussi G.
    Unraveling Mg2+-RNA binding with atomistic molecular dynamics
    RNA , 23 (5) pp. 628-638 (2017)
    doi: 10.1261/rna.060079.116
  • Mlynsky V., Bussi G.
    Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides
    RNA , 23 (5) pp. 712-720 (2017)
    doi: 10.1261/rna.060442.116
  • Suma A., Micheletti C.
    Pore translocation of knotted DNA rings
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 114 (15) (2017)
    doi: 10.1073/pnas.1701321114
  • Battisti A., Ciasca G., Grottesi A., Tenenbaum A.
    Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 19 (12) pp. 8435-8446 (2017)
    doi: 10.1039/c6cp07683a
  • Allegra M., Seyed-Allaei S., Pizzagalli F., Baftizadeh F., Maieron M., Reverberi C., Laio A., Amati D.
    fMRI Single Trial Discovery of Spatio-Temporal Brain Activity Patterns
    HUMAN BRAIN MAPPING , 38 (3) pp. 1421-1437 (2017)
    doi: 10.1002/hbm.23463
  • Orlandini E., Polles G., Marenduzzo D., Micheletti C.
    Self-assembly of knots and links
    JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT , (2017)
    doi: 10.1088/1742-5468/aa5bb5
  • D'Adamo G., Orlandini E., Micheletti C.
    Linking of Ring Polymers in Slit-Like Confinement
    MACROMOLECULES , 50 (4) pp. 1713-1718 (2017)
    doi: 10.1021/acs.macromol.6b02293
  • Grilli J., Adorisio M., Suweis S., Barabas G., Banavar J., Allesina S., Maritan A.
    Feasibility and coexistence of large ecological communities
    NATURE COMMUNICATIONS , 8 (2017)
    doi: 10.1038/ncomms14389
  • Everaers R., Grosberg A., Rubinstein M., Rosa A.
    Flory theory of randomly branched polymers
    SOFT MATTER , 13 (6) pp. 1223-1234 (2017)
    doi: 10.1039/c6sm02756c
  • Jackson S., Suma A., Micheletti C.
    How to fold intricately: using theory and experiments to unravel the properties of knotted proteins
    CURRENT OPINION IN STRUCTURAL BIOLOGY , 42 pp. 6-14 (2017)
    doi: 10.1016/j.sbi.2016.10.002
  • Pinamonti G., Zhao J., Condon D., Paul F., Noe F., Turner D., Bussi G.
    Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 13 (2) pp. 926-934 (2017)
    doi: 10.1021/acs.jctc.6b00982
  • Pezzotta A., Adorisio M., Celani A.
    From conformational spread to allosteric and cooperative models of E. coli flagellar motor
    JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT , (2017)
    doi: 10.1088/1742-5468/aa569e
  • Ponzoni L., Rossetti G., Maggi L., Giorgetti A., Carloni P., Micheletti C.
    Unifying view of mechanical and functional hotspots across class A GPCRs
    PLOS COMPUTATIONAL BIOLOGY , 13 (2) (2017)
    doi: 10.1371/journal.pcbi.1005381
  • Marenda M., Orlandini E., Micheletti C.
    Sorting ring polymers by knot type with modulated nanochannels
    SOFT MATTER , 13 (4) pp. 795-802 (2017)
    doi: 10.1039/c6sm02551j
  • Rosa A., Everaers R.
    Beyond Flory theory: Distribution functions for interacting lattice trees
    PHYSICAL REVIEW E , 95 (1) (2017)
    doi: 10.1103/PhysRevE.95.012117
  • Casalino L., Palermo G., Abdurakhmonova N., Rothlisberger U., Magistrato A.
    Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 13 (1) pp. 340-352 (2017)
    doi: 10.1021/acs.jctc.6b00905

2016

  • D'Adamo G., Dietler G., Micheletti C.
    Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains
    SOFT MATTER , 12 (32) pp. 6708-6715 (2016)
    doi: 10.1039/c6sm01327a
  • Sgrignani J., Cavalli A., Colombo G., Magistrato A.
    Enzymatic and Inhibition Mechanism of Human Aromatase (CYP19A1) Enzyme. A Computational Perspective from QM/MM and Classical Molecular Dynamics Simulations
    MINI-REVIEWS IN MEDICINAL CHEMISTRY , 16 (14) pp. 1112-1124 (2016)
    doi: 10.2174/1389557516666160623101129
  • Bisha I., Magistrato A.
    The molecular mechanism of secondary sodium symporters elucidated through the lens of the computational microscope
    RSC ADVANCES , 6 (12) pp. 9522-9540 (2016)
    doi: 10.1039/c5ra22131e
  • Marenda M., Zanardo M., Trovato A., Seno F., Squartini A.
    Modeling quorum sensing trade-offs between bacterial cell density and system extension from open boundaries
    SCIENTIFIC REPORTS , 6 (2016)
    doi: 10.1038/srep39142
  • Cesari A., Gil-Ley A., Bussi G.
    Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (12) pp. 6192-6200 (2016)
    doi: 10.1021/acs.jctc.6b00944
  • D'Adamo G., Pelissetto A.
    Improved model for mixtures of polymers and hard spheres
    JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL , 49 (50) (2016)
    doi: 10.1088/1751-8113/49/50/504006
  • Pellegrini F., Landes F., Laio A., Prestipino S., Tosatti E.
    Markov state modeling of sliding friction
    PHYSICAL REVIEW E , 94 (5) (2016)
    doi: 10.1103/PhysRevE.94.053001
  • Rosa A., Everaers R.
    Computer simulations of melts of randomly branching polymers
    JOURNAL OF CHEMICAL PHYSICS , 145 (16) (2016)
    doi: 10.1063/1.4965827
  • Di Stefano M., Paulsen J., Lien T., Hovig E., Micheletti C.
    Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization
    SCIENTIFIC REPORTS , 6 (2016)
    doi: 10.1038/srep35985
  • Bottaro S., Banas P., Sponer J., Bussi G.
    Free Energy Landscape of GAGA and UUCG RNA Tetraloops
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS , 7 (20) pp. 4032-4038 (2016)
    doi: 10.1021/acs.jpclett.6b01905
  • Casalino L., Magistrato A.
    Structural, dynamical and catalytic interplay between Mg2+ ions and RNA. Vices and virtues of atomistic simulations
    INORGANICA CHIMICA ACTA , 452 pp. 73-81 (2016)
    doi: 10.1016/j.ica.2016.02.011
  • Rosa M., Micciarelli M., Laio A., Baroni S.
    Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (9) pp. 4385-4389 (2016)
    doi: 10.1021/acs.jctc.6b00470
  • Kuhrova P., Best R., Bottaro S., Bussi G., Sponer J., Otyepka M., Banas P.
    Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (9) pp. 4534-4548 (2016)
    doi: 10.1021/acs.jctc.6b00300
  • Sarti E., Gladich I., Zamuner S., Correia B., Laio A.
    Protein-protein structure prediction by scoring molecular dynamics trajectories of putative poses
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , 84 (9) pp. 1312-1320 (2016)
    doi: 10.1002/prot.25079
  • Rosa A., Everaers R.
    Computer simulations of randomly branching polymers: annealed versus quenched branching structures
    JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL , 49 (34) (2016)
    doi: 10.1088/1751-8113/49/34/345001
  • Casalino L., Palermo G., Rothlisberger U., Magistrato A.
    Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 138 (33) pp. 10374-10377 (2016)
    doi: 10.1021/jacs.6b01363
  • Ghaemi Z., Alberga D., Carloni P., Laio A., Lattanzi G.
    Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (8) pp. 4093-4099 (2016)
    doi: 10.1021/acs.jctc.5b01126
  • Polles G., Odandini E., Micheletti C.
    Optimal Self-Assembly of Linked Constructs and Catenanes via Spatial Confinement
    ACS MACRO LETTERS , 5 (8) pp. 931-935 (2016)
    doi: 10.1021/acsmacrolett.6b00425
  • D'Adamo G., Pelissetto A., Pierleoni C.
    Phase Diagram and Structure of Mixtures of Large Colloids and Linear Polymers under Good-Solvent Conditions
    MACROMOLECULES , 49 (14) pp. 5266-5280 (2016)
    doi: 10.1021/acs.macromol.6b00600
  • Laio A., Martinelli G., Sanfilippo F.
    Metadynamics surfing on topology barriers: the CPN-1 case
    JOURNAL OF HIGH ENERGY PHYSICS , (7) (2016)
    doi: 10.1007/JHEP07(2016)089
  • Bottaro S., Gil-Ley A., Bussi G.
    RNA folding pathways in stop motion
    NUCLEIC ACIDS RESEARCH , 44 (12) pp. 5883-5891 (2016)
    doi: 10.1093/nar/gkw239
  • Rizzato F., Rodriguez A., Laio A.
    Non-Markovian effects on protein sequence evolution due to site dependent substitution rates
    BMC BIOINFORMATICS , 17 (2016)
    doi: 10.1186/s12859-016-1135-1
  • Palermo G., Magistrato A., Riedel T., von Erlach T., Davey C., Dyson P., Rothlisberger U.
    Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies
    CHEMMEDCHEM , 11 (12) pp. 1199-1210 (2016)
    doi: 10.1002/cmdc.201500478
  • Lousa D., Pinto A., Victor B., Laio A., Veiga A., Castanho M., Soares C.
    Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide
    SCIENTIFIC REPORTS , 6 (2016)
    doi: 10.1038/srep28099
  • Florescu A., Therizols P., Rosa A.
    Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure
    PLOS COMPUTATIONAL BIOLOGY , 12 (6) (2016)
    doi: 10.1371/journal.pcbi.1004987
  • Gil-Ley A., Bottaro S., Bussi G.
    Empirical Corrections to the Amber RNA Force Field with Target Metadynamics
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (6) pp. 2790-2798 (2016)
    doi: 10.1021/acs.jctc.6b00299
  • Cojoc G., Florescu A., Krull A., Klemm A., Pavin N., Julicher F., Tolic I.
    Paired arrangement of kinetochores together with microtubule pivoting and dynamics drive kinetochore capture in meiosis I
    SCIENTIFIC REPORTS , 6 (2016)
    doi: 10.1038/srep25736
  • Iwasa K., Florescu A.
    A molecule that detects the length of DNA by using chain fluctuations
    JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT , (2016)
    doi: 10.1088/1742-5468/2016/05/054030
  • Suma A., Cugliandolo L., Gonnella G.
    Tracer motion in an active dumbbell fluid
    JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT , (2016)
    doi: 10.1088/1742-5468/2016/05/054029
  • Allegra M., Giorda P., Lloyd S.
    Global coherence of quantum evolutions based on decoherent histories: Theory and application to photosynthetic quantum energy transport
    PHYSICAL REVIEW A , 93 (4) (2016)
    doi: 10.1103/PhysRevA.93.042312
  • Paloncyova M., Navratilova V., Berka K., Laio A., Otyepka M.
    Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 12 (4) pp. 2101-2109 (2016)
    doi: 10.1021/acs.jctc.6b00075
  • Del Carlo M., Capoferri D., Gladich I., Guida F., Forzato C., Navarini L., Compagnone D., Laio A., Berti F.
    In Silico Design of Short Peptides as Sensing Elements for Phenolic Compounds
    ACS SENSORS , 1 (3) pp. 279-286 (2016)
    doi: 10.1021/acssensors.5b00225
  • Nahali N., Rosa A.
    Density effects in entangled solutions of linear and ring polymers
    JOURNAL OF PHYSICS-CONDENSED MATTER , 28 (6) (2016)
    doi: 10.1088/0953-8984/28/6/065101
  • Burton A., Di Stefano M., Lehman N., Orland H., Micheletti C.
    The elusive quest for RNA knots
    RNA BIOLOGY , 13 (2) pp. 134-139 (2016)
    doi: 10.1080/15476286.2015.1132069

2015

  • Bussi G., Branduardi D.
    Free-Energy Calculations with Metadynamics: Theory and Practice
    REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28 , 28 pp. 1-49 (2015)
  • De Leo F., Magistrato A., Bonifazi D.
    Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies
    CHEMICAL SOCIETY REVIEWS , 44 (19) pp. 6916-6953 (2015)
    doi: 10.1039/c5cs00190k
  • Suma A., Rosa A., Micheletti C.
    Pore Translocation of Knotted Polymer Chains: How Friction Depends on Knot Complexity
    ACS MACRO LETTERS , 4 (12) pp. 1420-1424 (2015)
    doi: 10.1021/acsmacrolett.5b00747
  • Cugliandolo L., Gonnella G., Suma A.
    Fluctuations of rotational and translational degrees of freedom in an interacting active dumbbell system
    CHAOS SOLITONS & FRACTALS , 81 pp. 556-566 (2015)
    doi: 10.1016/j.chaos.2015.01.015
  • Di Palma F., Bottaro S., Bussi G.
    Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations
    BMC BIOINFORMATICS , 16 (2015)
    doi: 10.1186/1471-2105-16-S9-S6
  • Stadlbauer P., Kuhrova P., Banas P., Koca J., Bussi G., Trantirek L., Otyepka M., Sponer J.
    Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations
    NUCLEIC ACIDS RESEARCH , 43 (20) pp. 9626-9644 (2015)
    doi: 10.1093/nar/gkv994
  • Caraglio M., Micheletti C., Orlandini E.
    Stretching Response of Knotted and Unknotted Polymer Chains
    PHYSICAL REVIEW LETTERS , 115 (18) (2015)
    doi: 10.1103/PhysRevLett.115.188301
  • Granata D., Baftizadeh F., Habchi J., Galvagnion C., De Simone A., Camilloni C., Laio A., Vendruscolo M.
    The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments
    SCIENTIFIC REPORTS , 5 (2015)
    doi: 10.1038/srep15449
  • Gladich I., Rodriguez A., Enriquez R., Guida F., Berti F., Laio A.
    Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics
    JOURNAL OF PHYSICAL CHEMISTRY B , 119 (41) pp. 12963-12969 (2015)
    doi: 10.1021/acs.jpcb.5b06227
  • Sgrignani J., Iannuzzi M., Magistrato A.
    Role of Water in the Puzzling Mechanism of the Final Aromatization Step Promoted by the Human Aromatase Enzyme. Insights from QM/MM MD Simulations
    JOURNAL OF CHEMICAL INFORMATION AND MODELING , 55 (10) pp. 2218-2226 (2015)
    doi: 10.1021/acs.jcim.5b00249
  • Ma C., Martin-Samos L., Fabris S., Laio A., Piccinin S.
    QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS
    COMPUTER PHYSICS COMMUNICATIONS , 195 pp. 191-198 (2015)
    doi: 10.1016/j.cpc.2015.04.024
  • Menichetti R., D'Adamo G., Pelissetto A., Pierleoni C.
    Integral equation analysis of single-site coarse-grained models for polymer-colloid mixtures
    MOLECULAR PHYSICS , 113 (17-18) pp. 2629-2642 (2015)
    doi: 10.1080/00268976.2015.1039088
  • Perez-Villa A., Darvas M., Bussi G.
    ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.
    NUCLEIC ACIDS RESEARCH , 43 (18) pp. 8725-34 (2015)
    doi: 10.1093/nar/gkv872
  • Gladich I., Rodriguez A., Hong Enriquez R. P., Guida F., Berti F., Laio A.
    Designing High-Affinity Peptides for Organic Molecules by Explicit Solvent Molecular Dynamics.
    THE JOURNAL OF PHYSICAL CHEMISTRY. B , 119 (41) pp. 12963-9 (2015)
    doi: 10.1021/acs.jpcb.5b06227
  • Ma C., Martin-Samos L., Fabris S., Laio A., Piccinin S.
    QMMMW: A wrapper for QM/MM simulations with QUANTUM ESPRESSO and LAMMPS
    COMPUTER PHYSICS COMMUNICATIONS , 195 pp. 191-198 (2015)
    doi: 10.1016/j.cpc.2015.04.024
  • Suma A., Orlandini E., Micheletti C.
    Knotting dynamics of DNA chains of different length confined in nanochannels.
    JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL , 27 (35) pp. 354102-354102 (2015)
    doi: 10.1088/0953-8984/27/35/354102
  • D'Adamo G., Micheletti C.
    Molecular Crowding Increases Knots Abundance in Linear Polymers
    MACROMOLECULES , 48 (17) pp. 6337-6346 (2015)
    doi: 10.1021/acs.macromol.5b01323
  • Pinamonti G., Bottaro S., Micheletti C., Bussi G.
    Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments
    NUCLEIC ACIDS RESEARCH , 43 (15) pp. 7260-7269 (2015)
    doi: 10.1093/nar/gkv708
  • D'Adamo G., Menichetti R., Pelissetto A., Pierleoni C.
    Coarse-graining polymer solutions: A critical appraisal of single- and multi-site models
    EUROPEAN PHYSICAL JOURNAL-SPECIAL TOPICS , 224 (12) pp. 2239-2267 (2015)
    doi: 10.1140/epjst/e2015-02410-3
  • Ponzoni L., Polles G., Carnevale V., Micheletti C.
    SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets
    STRUCTURE , 23 (8) pp. 1516-1525 (2015)
    doi: 10.1016/j.str.2015.05.022
  • Cugliandolo L. F., Gonnella G., Suma A.
    Rotational and translational diffusion in an interacting active dumbbell system
    PHYSICAL REVIEW E , 91 (6) (2015)
    doi: 10.1103/PhysRevE.91.062124
  • Zhang T., Nguyen P. H., Nasica-Labouze J., Mu Y., Derreumaux P.
    Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering
    JOURNAL OF PHYSICAL CHEMISTRY B , 119 (23) pp. 6941-6951 (2015)
    doi: 10.1021/acs.jpcb.5b03381
  • Sgrignani J., Magistrato A.
    QM/MM MD Simulations on the Enzymatic Pathway of the Human Flap Endonuclease (hFEN1) Elucidating Common Cleavage Pathways to RNase H Enzymes
    ACS CATALYSIS , 5 (6) pp. 3864-3875 (2015)
    doi: 10.1021/acscatal.5b00178
  • Gladich I., Francisco J. S., Buszek R. J., Vazdar M., Carignano M. A., Shepson P. B.
    Ab Initio Study of the Reaction of Ozone with Bromide Ion
    JOURNAL OF PHYSICAL CHEMISTRY A , 119 (19) pp. 4482-4488 (2015)
    doi: 10.1021/jp5101279
  • Nasica-Labouze J., Nguyen P. H., Sterpone F., Berthoumieu O., Buchete N., Cote S., De Simone A., Doig A. J., Faller P., Garcia A., Laio A., Li M. S., Melchionna S., Mousseau N., Mu Y., Paravastu A., Pasquali S., Rosenman D. J., Strodel B., Tarus B., Viles J. H., Zhang T., Wang C., Derreumaux P.
    Amyloid beta Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies
    CHEMICAL REVIEWS , 115 (9) pp. 3518-3563 (2015)
    doi: 10.1021/cr500638n
  • D'Adamo G., Marenduzzo D., Micheletti C., Orlandini E.
    Electric Field Controlled Columnar and Planar Patterning of Cholesteric Colloids
    PHYSICAL REVIEW LETTERS , 114 (17) (2015)
    doi: 10.1103/PhysRevLett.114.177801
  • Gonnella G., Marenduzzo D., Suma A., Tiribocchi A.
    Motility-induced phase separation and coarsening in active matter
    COMPTES RENDUS PHYSIQUE , 16 (3) pp. 316-331 (2015)
    doi: 10.1016/j.crhy.2015.05.001
  • Sarti E., Granata D., Seno F., Trovato A., Laio A.
    Native fold and docking pose discrimination by the same residue-based scoring function
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , 83 (4) pp. 621-630 (2015)
    doi: 10.1002/prot.24764
  • Zamuner S., Rodriguez A., Seno F., Trovato A.
    An Efficient Algorithm to Perform Local Concerted Movements of a Chain Molecule
    PLOS ONE , 10 (3) (2015)
    doi: 10.1371/journal.pone.0118342
  • Polles G., Marenduzzo D., Orlandini E., Micheletti C.
    Self-assembling knots of controlled topology by designing the geometry of patchy templates
    NATURE COMMUNICATIONS , 6 (2015)
    doi: 10.1038/ncomms7423
  • Gil-Ley A., Bussi G.
    Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 11 (3) pp. 1077-1085 (2015)
    doi: 10.1021/ct5009087
  • Micheletti C., Di Stefano M., Orland H.
    Absence of knots in known RNA structures
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 112 (7) pp. 2052-2057 (2015)
    doi: 10.1073/pnas.1418445112
  • Tubiana L., Bozic A., Micheletti C., Podgornik R.
    Synonymous Mutations Reduce Genome Compactness in Icosahedral ssRNA Viruses
    BIOPHYSICAL JOURNAL , 108 (1) pp. 194-202 (2015)
    doi: 10.1016/j.bpj.2014.10.070
  • Angel Martinez-Gonzalez J., Rodriguez A., Pilar Puyuelo M., Gonzalez M., Martinez R.
    Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease
    CHEMICAL PHYSICS LETTERS , 619 pp. 97-102 (2015)
    doi: 10.1016/j.cplett.2014.11.041
  • De Leo F., Magistrato A., Bonifazi D.
    Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies
    CHEMICAL SOCIETY REVIEWS , 44 (19) pp. 6916-6953 (2015)
    doi: 10.1039/c5cs00190k
  • Fabian B., Darvas M., Picaud S., Sega M., Jedlovszky P.
    The effect of anaesthetics on the properties of a lipid membrane in the biologically relevant phase: a computer simulation study
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 17 (22) pp. 14750-14760 (2015)
    doi: 10.1039/c5cp00851d
  • Di Palma F., Colizzi F., Bussi G.
    Using reweighted pulling simulations to characterize conformational changes in riboswitches.
    METHODS IN ENZYMOLOGY , 553 pp. 139-62 (2015)
    doi: 10.1016/bs.mie.2014.10.055
  • Ferrarotti M. J., Bottaro S., Perez-Villa A., Bussi G.
    Accurate Multiple Time Step in Biased Molecular Simulations
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 11 (1) pp. 139-146 (2015)
    doi: 10.1021/ct5007086

2014

  • D'Adamo G., Pelissetto A., Pierleoni C.
    Accurate coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions
    JOURNAL OF CHEMICAL PHYSICS , 141 (24) (2014)
    doi: 10.1063/1.4904392
  • Valet M., Rosa A.
    Viscoelasticity of model interphase chromosomes
    JOURNAL OF CHEMICAL PHYSICS , 141 (24) (2014)
    doi: 10.1063/1.4903996
  • Bisha I., Rodriguez A., Laio A., Magistrato A.
    Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT
    PLOS COMPUTATIONAL BIOLOGY , 10 (12) (2014)
    doi: 10.1371/journal.pcbi.1004017
  • Bottaro S., Di Palma F., Bussi G.
    The role of nucleobase interactions in RNA structure and dynamics
    NUCLEIC ACIDS RESEARCH , 42 (21) pp. 13306-13314 (2014)
    doi: 10.1093/nar/gku972
  • Suma A., Gonnella G., Laghezza G., Lamura A., Mossa A., Cugliandolo L. F.
    Dynamics of a homogeneous active dumbbell system
    PHYSICAL REVIEW E , 90 (5) (2014)
    doi: 10.1103/PhysRevE.90.052130
  • Musiani F., Rossetti G., Capece L., Gerger T. M., Micheletti C., Varani G., Carloni P.
    Molecular Dynamics Simulations Identify Time Scale of Conformational Changes Responsible for Conformational Selection in Molecular Recognition of HIV-1 Transactivation Responsive RNA
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 136 (44) pp. 15631-15637 (2014)
    doi: 10.1021/0507812y
  • Sgrignani J., Bon M., Colombo G., Magistrato A.
    Computational Approaches Elucidate the Allosteric Mechanism of Human Aromatase Inhibition: A Novel Possible Route to Small-Molecule Regulation of CYP450s Activities?
    JOURNAL OF CHEMICAL INFORMATION AND MODELING , 54 (10) pp. 2856-2868 (2014)
    doi: 10.1021/ci500425y
  • Jaafar R., Pignedoli C. A., Bussi G., Ait-Mansour K., Groening O., Amaya T., Hirao T., Fasel R., Ruffieux P.
    Bowl Inversion of Surface-Adsorbed Sumanene
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 136 (39) pp. 13666-13671 (2014)
    doi: 10.1021/ja504126z
  • Kania R., Malongwe J. K., Nachtigallova D., Krausko J., Gladich I., Roeselova M., Heger D., Klan P.
    Spectroscopic Properties of Benzene at the Air-Ice Interface: A Combined Experimental-Computational Approach
    JOURNAL OF PHYSICAL CHEMISTRY A , 118 (35) pp. 7535-7547 (2014)
    doi: 10.1021/jp501094n
  • Micheletti C., Orlandini E.
    Knotting and Unknotting Dynamics of DNA Strands in Nanochannels
    ACS MACRO LETTERS , 3 (9) pp. 876-880 (2014)
    doi: 10.1021/mz500402s
  • Vargiu A. V., Magistrato A.
    Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations
    CHEMMEDCHEM , 9 (9) pp. 1966-1981 (2014)
    doi: 10.1002/cmdc.201402203
  • Franco D., Vargiu A. V., Magistrato A.
    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
    INORGANIC CHEMISTRY , 53 (15) pp. 7999-8008 (2014)
    doi: 10.1021/ic5008523
  • D'Adamo G., Pelissetto A., Pierleoni C.
    Phase diagram of mixtures of colloids and polymers in the thermal crossover from good to theta solvent
    JOURNAL OF CHEMICAL PHYSICS , 141 (2) (2014)
    doi: 10.1063/1.4885818
  • Rodriguez A., Laio A.
    Clustering by fast search and find of density peaks
    SCIENCE , 344 (6191) pp. 1492-1496 (2014)
    doi: 10.1126/science.1242072
  • Rosa A., Everaers R.
    Ring Polymers in the Melt State: The Physics of Crumpling
    PHYSICAL REVIEW LETTERS , 112 (11) (2014)
    doi: 10.1103/PhysRevLett.112.118302
  • Prestipino S., Laio A., Tosatti E.
    Shape and area fluctuation effects on nucleation theory
    JOURNAL OF CHEMICAL PHYSICS , 140 (9) (2014)
    doi: 10.1063/1.4866971
  • Bussi G.
    Hamiltonian replica exchange in GROMACS: a flexible implementation
    MOLECULAR PHYSICS , 112 (3-4) pp. 379-384 (2014)
    doi: 10.1080/00268976.2013.824126
  • Tribello G. A., Bonomi M., Branduardi D., Camilloni C., Bussi G.
    PLUMED 2: New feathers for an old bird
    COMPUTER PHYSICS COMMUNICATIONS , 185 (2) pp. 604-613 (2014)
    doi: 10.1016/j.cpc.2013.09.018
  • Di Palma F., Colizzi F., Bussi G.
    Role of Magnesium Ions and Ligand Stacking in the Adenine Riboswitch Folding
    BIOPHYSICAL JOURNAL , 106 (2) (2014)
  • Bisha I., Rodriguez A., Sgrignani J., Magistrato A., Laio A.
    Sodium-Galactose Transporter: The First Steps of the Transport Mechanism Investigated by Molecular Dynamics
    BIOPHYSICAL JOURNAL , 106 (2) (2014)
  • De Leo F., Sgrignani J., Magistrato A., Bonifazi D.
    Structural and Dynamical Properties of Monoclonal Antibodies Immobilized on CNTs: A Computational Study
    BIOPHYSICAL JOURNAL , 106 (2) (2014)
  • Napolitano L. M. R., Bisha I., Arcangeletti M., Marchesi A., De March M., Onesti S., Laio A., Torre V.
    Mechanism of Ionic Permeation in the Mimics of CNG Channels: A Structural, Functional and Computational Analysis
    BIOPHYSICAL JOURNAL , 106 (2) (2014)
  • Di Stefano M., Tubiana L., Di Ventra M., Micheletti C.
    Driving knots on DNA with AC/DC electric fields: topological friction and memory effects
    SOFT MATTER , 10 (34) pp. 6491-6498 (2014)
    doi: 10.1039/c4sm00160e
  • Rosa A., Zimmer C.
    Computational Models of Large-Scale Genome Architecture
    NEW MODELS OF THE CELL NUCLEUS: CROWDING, ENTROPIC FORCES, PHASE SEPARATION, AND FRACTALS , 307 pp. 275-349 (2014)
    doi: 10.1016/B978-0-12-800046-5.00009-6
  • Colizzi F., Lamontagne A., Lafontaine D. A., Bussi G.
    Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays.
    METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) , 1103 pp. 141-51 (2014)
    doi: 10.1007/978-1-62703-730-3_11
  • Darvas M., Jorge M., Cordeiro M. N. D. S., Jedlovszky P.
    Calculation of the intrinsic solvation free energy profile of methane across a liquid/liquid interface in computer simulations
    JOURNAL OF MOLECULAR LIQUIDS , 189 pp. 39-43 (2014)
    doi: 10.1016/j.molliq.2013.05.029
  • Kertesz J., Darvas M., Jedlovszky P., Horvai G.
    Role of the fluidity of a liquid phase in determining the surface properties of the opposite phase (Reprinted from Journal of Molecular Liquids, Vol 186, Pages 7-13, 2013)
    JOURNAL OF MOLECULAR LIQUIDS , 189 pp. 122-128 (2014)
    doi: 10.1016/j.molliq.2013.06.009
  • Abrams C., Bussi G.
    Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
    ENTROPY , 16 (1) pp. 163-199 (2014)
    doi: 10.3390/e16010163

2013

  • Sarti E., Zamuner S., Cossio P., Laio A., Seno F., Trovato A.
    BACHSCORE. A tool for evaluating efficiently and reliably the quality of large sets of protein structures
    COMPUTER PHYSICS COMMUNICATIONS , 184 (12) pp. 2860-2865 (2013)
    doi: 10.1016/j.cpc.2013.07.019
  • Facchetti G., Altafini C.
    Partial inhibition and bilevel optimization in flux balance analysis
    BMC BIOINFORMATICS , 14 (2013)
    doi: 10.1186/1471-2105-14-344
  • Polles G., Indelicato G., Potestio R., Cermelli P., Twarock R., Micheletti C.
    Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
    PLOS COMPUTATIONAL BIOLOGY , 9 (11) (2013)
    doi: 10.1371/journal.pcbi.1003331
  • Di Palma F., Colizzi F., Bussi G.
    Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
    RNA-A PUBLICATION OF THE RNA SOCIETY , 19 (11) pp. 1517-1524 (2013)
    doi: 10.1261/rna.040493.113
  • De Leo F., Sgrignani J., Bonifazi D., Magistrato A.
    Structural and Dynamic Properties of Monoclonal Antibodies Immobilized on CNTs: A Computational Study
    CHEMISTRY-A EUROPEAN JOURNAL , 19 (37) pp. 12281-12293 (2013)
    doi: 10.1002/chem.201301376
  • Micheletti C., Marenduzzo D., Orlandini E., Stasiak A., Sumners D. W.
    Knotted strands of life: DNA knotting inside viral capsids
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 246 (2013)
  • Mancini F., Wiggins C. H., Marsili M., Walczak A. M.
    Time-dependent information transmission in a model regulatory circuit
    PHYSICAL REVIEW E , 88 (2) (2013)
    doi: 10.1103/PhysRevE.88.022708
  • Marega R., De Leo F., Pineux F., Sgrignani J., Magistrato A., Naik A. D., Garcia Y., Flamant L., Michiels C., Bonifazi D.
    Functionalized Fe-Filled Multiwalled Carbon Nanotubes as Multifunctional Scaffolds for Magnetization of Cancer Cells
    ADVANCED FUNCTIONAL MATERIALS , 23 (25) pp. 3173-3184 (2013)
    doi: 10.1002/adfm.201202898
  • Bisha I., Laio A., Magistrato A., Giorgetti A., Sgrignani J.
    Sodium-Galactose Transporter: first steps of transport mechanism investigated by molecular dynamics
    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS , 42 (2013)
  • Colizzi F., Levy Y., Bussi G.
    Symmetry and asymmetry in the unwinding of nucleic acids
    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS , 42 (2013)
  • Ianeselli L., Grenci G., Tormen M., Casalis L., Laio A.
    Development of Electrochemical Impedance Immunosensors as Point of Care Medical Diagnostic Tools
    EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS , 42 (2013)
  • Mancini C., Roncaglia P., Brussino A., Stevanin G., Lo Buono N., Krmac H., Maltecca F., Gazzano E., Stella A. B., Calvaruso M. A., Iommarini L., Cagnoli C., Forlani S., Le Ber I., Durr A., Brice A., Ghigo D., Casari G., Porcelli A. M., Funaro A., Gasparre G., Gustincich S., Brusco A.
    Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways
    BMC MEDICAL GENOMICS , 6 (2013)
    doi: 10.1186/1755-8794-6-22
  • Franco D., Sgrignani J., Bussi G., Magistrato A.
    Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations
    JOURNAL OF CHEMICAL INFORMATION AND MODELING , 53 (6) pp. 1371-1387 (2013)
    doi: 10.1021/ci4001647
  • Capasso V., Morale D., Facchetti G.
    Randomness in self-organized phenomena. A case study: Retinal angiogenesis
    BIOSYSTEMS , 112 (3) pp. 292-297 (2013)
    doi: 10.1016/j.biosystems.2013.01.003
  • Tubiana L., Rosa A., Fragiacomo F., Micheletti C.
    Spontaneous Knotting and Unknotting of Flexible Linear Polymers: Equilibrium and Kinetic Aspects
    MACROMOLECULES , 46 (9) pp. 3669-3678 (2013)
    doi: 10.1021/ma4002963
  • Facchetti G., Iacono G., De Palo G., Altafini C.
    A rate-distortion theory for gene regulatory networks and its application to logic gate consistency
    BIOINFORMATICS , 29 (9) pp. 1166-1173 (2013)
    doi: 10.1093/bioinformatics/btt116
  • Musiani F., Ippoliti E., Micheletti C., Carloni P., Ciurli S.
    Conformational Fluctuations of UreG, an Intrinsically Disordered Enzyme
    BIOCHEMISTRY , 52 (17) pp. 2949-2954 (2013)
    doi: 10.1021/bi4001744
  • Granata D., Camilloni C., Vendruscolo M., Laio A.
    Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 110 (17) pp. 6817-6822 (2013)
    doi: 10.1073/pnas.1218350110
  • Baftizadeh F., Pietrucci F., Biarnes X., Laio A.
    Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-beta
    PHYSICAL REVIEW LETTERS , 110 (16) (2013)
    doi: 10.1103/PhysRevLett.110.168103
  • Colizzi F., Bussi G.
    RNA unwinding: What we can learn from atomistic simulations
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 245 (2013)
  • Di Palma F., Colizzi F., Bussi G.
    Conformational transitions in adenine sensing riboswitch: A computational study
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 245 (2013)
  • Branduardi D., Bussi G., Parrinello M.
    Metadynamics with adaptive Gaussians
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 245 (2013)
  • Do T. N., Carloni P., Varani G., Bussi G.
    RNA/peptide binding driven by electrostatics: Insights from bi-directional pulling simulations
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 245 (2013)
  • Rosa A.
    Topological constraints and chromosome organization in eukaryotes: a physical point of view
    BIOCHEMICAL SOCIETY TRANSACTIONS , 41 pp. 612-615 (2013)
    doi: 10.1042/BST20120330
  • Beccara S. A., Skrbic T., Covino R., Micheletti C., Faccioli P.
    Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
    PLOS COMPUTATIONAL BIOLOGY , 9 (3) (2013)
    doi: 10.1371/journal.pcbi.1003002
  • Sgrignani J., Magistrato A.
    First-Principles Modeling of Biological Systems and Structure-Based Drug-Design
    CURRENT COMPUTER-AIDED DRUG DESIGN , 9 (1) pp. 15-34 (2013)
  • Livolant F., Lorman V., Marsili M., Micheletti C., Podgornik R.
    Special issue on physical virology
    JOURNAL OF BIOLOGICAL PHYSICS , 39 (2) pp. 161-162 (2013)
    doi: 10.1007/s10867-013-9320-1
  • Orlandini E., Micheletti C.
    Knotting of linear DNA in nano-slits and nano-channels: a numerical study
    JOURNAL OF BIOLOGICAL PHYSICS , 39 (2) pp. 267-275 (2013)
    doi: 10.1007/s10867-013-9305-0
  • Micheletti C.
    Comparing proteins by their internal dynamics: Exploring structure-function relationships beyond static structural alignments
    PHYSICS OF LIFE REVIEWS , 10 (1) pp. 1-26 (2013)
    doi: 10.1016/j.plrev.2012.10.009
  • Micheletti C.
    Reply to comments on "Comparing proteins by their internal dynamics: Exploring structure-function relationships beyond static structural alignments"
    PHYSICS OF LIFE REVIEWS , 10 (1) pp. 39-40 (2013)
    doi: 10.1016/j.plrev.2012.11.001
  • Di Stefano M., Rosa A., Belcastro V., di Bernardo D., Micheletti C.
    Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19
    PLOS COMPUTATIONAL BIOLOGY , 9 (3) (2013)
    doi: 10.1371/journal.pcbi.1003019
  • Do T. N., Carloni P., Varani G., Bussi G.
    RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 9 (3) pp. 1720-1730 (2013)
    doi: 10.1021/ct3009914
  • Prestipino S., Laio A., Tosatti E.
    A fingerprint of surface-tension anisotropy in the free-energy cost of nucleation
    JOURNAL OF CHEMICAL PHYSICS , 138 (6) (2013)
    doi: 10.1063/1.4790635
  • De Palo G., Facchetti G., Mazzolini M., Menini A., Torre V., Altafini C.
    Common dynamical features of sensory adaptation in photoreceptors and olfactory sensory neurons.
    SCIENTIFIC REPORTS , 3 (2013)
  • De Palo G., Facchetti G., Mazzolini M., Menini A., Torre V., Altafini C.
    Common dynamical features of sensory adaptation in photoreceptors and olfactory sensory neurons
    SCIENTIFIC REPORTS , 3 (2013)
    doi: 10.1038/srep01251
  • Bon M., Micheletti C., Orland H.
    McGenus: a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots
    NUCLEIC ACIDS RESEARCH , 41 (3) pp. 1895-1900 (2013)
    doi: 10.1093/nar/gks1204
  • Bisha I., Laio A., Magistrato A., Giorgetti A., Sgrignani J.
    A Candidate Ion-Retaining State in the Inward-Facing Conformation of Sodium/Galactose Symporter: Clues from Atomistic Simulations
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 9 (2) pp. 1240-1246 (2013)
    doi: 10.1021/ct3008233
  • Granata D., Baghal F. B., Camilloni C., Vendruscolo M., Laio A.
    Thermodynamics of an Intrinsically Disordered Protein by Atomistic Simulations
    BIOPHYSICAL JOURNAL , 104 (2) (2013)
  • Enriquez R. P. H., Pavan S., Benedetti F., Tossi A., Savoini A., Berti F., Laio A.
    Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics and Monte Carlo Approach
    BIOPHYSICAL JOURNAL , 104 (2) (2013)

2012

  • Hu X. L., Piccinin S., Laio A., Fabris S.
    Atomistic Structure of Cobalt-Phosphate Nanoparticles for Catalytic Water Oxidation
    ACS NANO , 6 (12) pp. 10497-10504 (2012)
    doi: 10.1021/nn3044325
  • Capasso V., Morale D., Facchetti G.
    The role of stochasticity in a model of retinal angiogenesis
    IMA JOURNAL OF APPLIED MATHEMATICS , 77 (6) pp. 729-747 (2012)
    doi: 10.1093/imamat/hxs050
  • Gobbo G., Laio A., Maleki A., Baroni S.
    Absolute Transition Rates for Rare Events from Dynamical Decoupling of Reaction Variables
    PHYSICAL REVIEW LETTERS , 109 (15) (2012)
    doi: 10.1103/PhysRevLett.109.150601
  • Facchetti G., Iacono G., Altafini C.
    Exploring the low-energy landscape of large-scale signed social networks
    PHYSICAL REVIEW E , 86 (3) (2012)
    doi: 10.1103/PhysRevE.86.036116
  • Yusuff O. K., Babalola J. O., Bussi G., Raugei S.
    Role of the Subunit Interactions in the Conformational Transitions in Adult Human Hemoglobin: An Explicit Solvent Molecular Dynamics Study
    JOURNAL OF PHYSICAL CHEMISTRY B , 116 (36) pp. 11004-11009 (2012)
    doi: 10.1021/jp3022908
  • Rosa A., Di Ventra M., Micheletti C.
    Topological Jamming of Spontaneously Knotted Polyelectrolyte Chains Driven Through a Nanopore
    PHYSICAL REVIEW LETTERS , 109 (11) (2012)
    doi: 10.1103/PhysRevLett.109.118301
  • Facchetti G., Zampieri M., Altafini C.
    Predicting and characterizing selective multiple drug treatments for metabolic diseases and cancer
    BMC SYSTEMS BIOLOGY , 6 (2012)
    doi: 10.1186/1752-0509-6-115
  • D'Angelo P., Della Longa S., Arcovito A., Mancini G., Zitolo A., Chillemi G., Giachin G., Legname G., Benetti F.
    Effects of the Pathological Q212P Mutation on Human Prion Protein Non-Octarepeat Copper-Binding Site
    BIOCHEMISTRY , 51 (31) pp. 6068-6079 (2012)
    doi: 10.1021/bi300233n
  • Ghaemi Z., Minozzi M., Carloni P., Laio A.
    A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations
    JOURNAL OF PHYSICAL CHEMISTRY B , 116 (29) pp. 8714-8721 (2012)
    doi: 10.1021/jp301083h
  • Branduardi D., Bussi G., Parrinello M.
    Metadynamics with Adaptive Gaussians
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 8 (7) pp. 2247-2254 (2012)
    doi: 10.1021/ct3002464
  • Skrbic T., Micheletti C., Faccioli P.
    The Role of Non-Native Interactions in the Folding of Knotted Proteins
    PLOS COMPUTATIONAL BIOLOGY , 8 (6) (2012)
    doi: 10.1371/journal.pcbi.1002504
  • Sgrignani J., Magistrato A.
    Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study
    JOURNAL OF CHEMICAL INFORMATION AND MODELING , 52 (6) pp. 1595-1606 (2012)
    doi: 10.1021/ci300151h
  • Prestipino S., Laio A., Tosatti E.
    Systematic Improvement of Classical Nucleation Theory
    PHYSICAL REVIEW LETTERS , 108 (22) (2012)
    doi: 10.1103/PhysRevLett.108.225701
  • Cossio P., Granata D., Laio A., Seno F., Trovato A.
    A simple and efficient statistical potential for scoring ensembles of protein structures
    SCIENTIFIC REPORTS , 2 (2012)
    doi: 10.1038/srep00351
  • Sgrignani J., Magistrato A., Dal Peraro M., Vila A. J., Carloni P., Pierattelli R.
    On the active site of mononuclear B1 metallo beta-lactamases: a computational study
    JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN , 26 (4) pp. 425-435 (2012)
    doi: 10.1007/s10822-012-9571-0
  • Colizzi F., Bussi G.
    RNA Unwinding from Reweighted Pulling Simulations
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 134 (11) pp. 5173-5179 (2012)
    doi: 10.1021/ja210531q
  • Morra G., Potestio R., Micheletti C., Colombo G.
    Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations
    PLOS COMPUTATIONAL BIOLOGY , 8 (3) (2012)
    doi: 10.1371/journal.pcbi.1002433
  • Enriquez R. P. H., Pavan S., Benedetti F., Tossi A., Savoini A., Berti F., Laio A.
    Designing Short Peptides with High Affinity for Organic Molecules: A Combined Docking, Molecular Dynamics, And Monte Carlo Approach
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION , 8 (3) pp. 1121-1128 (2012)
    doi: 10.1021/ct200873y
  • Baftizadeh F., Biarnes X., Pietrucci F., Affinito F., Laio A.
    Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 134 (8) pp. 3886-3894 (2012)
    doi: 10.1021/ja210826a
  • Micheletti C., Orlandini E.
    Numerical Study of Linear and Circular Model DNA Chains Confined in a Slit: Metric and Topological Properties
    MACROMOLECULES , 45 (4) pp. 2113-2121 (2012)
    doi: 10.1021/ma202503k
  • Sgrignani J., Magistrato A.
    The Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study
    JOURNAL OF PHYSICAL CHEMISTRY B , 116 (7) pp. 2259-2268 (2012)
    doi: 10.1021/jp206475d
  • Vargiu A. V., Magistrato A.
    Detecting DNA Mismatches with Metallo-Insertors: A Molecular Simulation Study
    INORGANIC CHEMISTRY , 51 (4) pp. 2046-2057 (2012)
    doi: 10.1021/ic201659v
  • Chiriano G., De Simone A., Mancini F., Perez D. I., Cavalli A., Bolognesi M. L., Legname G., Martinez A., Andrisano V., Carloni P., Roberti M.
    A small chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: Structure-based design, synthesis, and biological evaluation
    EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY , 48 pp. 206-213 (2012)
    doi: 10.1016/j.ejmech.2011.12.016
  • Valbuena A., Bussi G.
    Understanding CNG Channels Gating Process by MD Simulations
    BIOPHYSICAL JOURNAL , 102 (3) (2012)
  • Baghal F. B., Biarnes X., Pietrucci F., Laio A., Affinito F.
    Simulation of Amyloid Nucleation with Bias-Exchange Metadynamics
    BIOPHYSICAL JOURNAL , 102 (3) (2012)
  • Bafghi Z. G., Laio A., Carloni P.
    Atomistic Simulation Studies of the Permeation of Organic Molecules Through Lipid Membranes
    BIOPHYSICAL JOURNAL , 102 (3) (2012)
  • Tubiana L., Orlandini E., Micheletti C.
    Multiscale Entanglement in Spherically Confined DNA Rings
    BIOPHYSICAL JOURNAL , 102 (3) (2012)
  • Everaers R., Rosa A.
    Multi-scale modeling of diffusion-controlled reactions in polymers: Renormalisation of reactivity parameters
    JOURNAL OF CHEMICAL PHYSICS , 136 (1) (2012)
    doi: 10.1063/1.3673444
  • Benetti F., Della Longa S., Arcovito A., Mancini G., Zitolo A., Chillemi G., Giachin G., Legname G., D'Angelo P.
    Effects of the pathological Q212P mutation on human prion protein non-octarepeat copper binding site
    PRION , 6 pp. 81-82 (2012)
  • Micheletti C., Orlandini E.
    Knotting and metric scaling properties of DNA confined in nano-channels: a Monte Carlo study
    SOFT MATTER , 8 (42) pp. 10959-10968 (2012)
    doi: 10.1039/c2sm26401c
  • Bosco A., Bano F., Parisse P., Casalis L., DeSimone A., Micheletti C.
    Hybridization in nanostructured DNA monolayers probed by AFM: theory versus experiment
    NANOSCALE , 4 (5) pp. 1734-1741 (2012)
    doi: 10.1039/c2nr11662f
  • Biarnes X., Pietrucci F., Marinelli F., Laio A.
    METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations
    COMPUTER PHYSICS COMMUNICATIONS , 183 (1) pp. 203-211 (2012)
    doi: 10.1016/j.cpc.2011.08.020

2011

  • Bolognesi M. L., 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.
    Synthesis of Monomeric Derivatives To Probe Memoquin's Bivalent Interactions
    JOURNAL OF MEDICINAL CHEMISTRY , 54 (24) pp. 8299-8304 (2011)
    doi: 10.1021/jm200691d
  • Rosa A., Orlandini E., Tubiana L., Micheletti C.
    Structure and Dynamics of Ring Polymers: Entanglement Effects Because of Solution Density and Ring Topology
    MACROMOLECULES , 44 (21) pp. 8668-8680 (2011)
    doi: 10.1021/ma201827f
  • Crespo Y., Laio A., Santoro G. E., Tosatti E.
    Theory of the reentrant quantum rotational phase transition in high-pressure HD
    PHYSICAL REVIEW B , 84 (14) (2011)
    doi: 10.1103/PhysRevB.84.144119
  • Tubiana L., Orlandini E., Micheletti C.
    Multiscale Entanglement in Ring Polymers under Spherical Confinement
    PHYSICAL REVIEW LETTERS , 107 (18) (2011)
    doi: 10.1103/PhysRevLett.107.188302
  • Rossetti G., Cossio P., Laio A., Carloni P.
    Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations
    FEBS LETTERS , 585 (19) pp. 3086-3089 (2011)
    doi: 10.1016/j.febslet.2011.08.036
  • Benedetti F., Micheletti C., Bussi G., Sekatskii S. K., Dietler G.
    Nonkinetic Modeling of the Mechanical Unfolding of Multimodular Proteins: Theory and Experiments
    BIOPHYSICAL JOURNAL , 101 (6) pp. 1504-1512 (2011)
    doi: 10.1016/j.bpj.2011.07.047
  • Raiteri P., Gale J. D., Bussi G.
    Reactive force field simulation of proton diffusion in BaZrO3 using an empirical valence bond approach
    JOURNAL OF PHYSICS-CONDENSED MATTER , 23 (33) (2011)
    doi: 10.1088/0953-8984/23/33/334213
  • Cardamone L., Laio A., Torre V., Shahapure R., DeSimone A.
    Cytoskeletal actin networks in motile cells are critically self-organized systems synchronized by mechanical interactions
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA , 108 (34) pp. 13978-13983 (2011)
    doi: 10.1073/pnas.1100549108
  • Micheletti C., Marenduzzo D., Orlandini E.
    Polymers with spatial or topological constraints: Theoretical and computational results
    PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS , 504 (1) pp. 1-73 (2011)
    doi: 10.1016/j.physrep.2011.03.003
  • Martin-Samos L., Bussi G., Ruini A., Molinari E., Caldas M. J.
    SiO2 in density functional theory and beyond
    PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS , 248 (5) pp. 1061-1066 (2011)
    doi: 10.1002/pssb.201046283
  • Chiriano G., Sartini A., Mancini F., Andrisano V., Bolognesi M. L., Roberti M., Recanatini M., Carloni P., Cavalli A.
    Sequential Virtual Screening Approach to the Identification of Small Organic Molecules as Potential BACE-1 Inhibitors
    CHEMICAL BIOLOGY & DRUG DESIGN , 77 (4) pp. 268-271 (2011)
    doi: 10.1111/j.1747-0285.2011.01087.x
  • Zhai Y., Laio A., Tosatti E., Gong X.
    Finite Temperature Properties of Clusters by Replica Exchange Metadynamics: The Water Nonamer
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 133 (8) pp. 2535-2540 (2011)
    doi: 10.1021/ja1076316
  • Carnevale V., Micheletti C., Pontiggia F., Potestio R.
    Bridging the Atomic and Coarse-Grained Descriptions of Collective Motions in Proteins
    MULTISCALE APPROACHES TO PROTEIN MODELING , pp. 159-178 (2011)
    doi: 10.1007/978-1-4419-6889-0_7
  • Sgrignani J., Franco D., Magistrato A.
    Theoretical Studies of Homogeneous Catalysts Mimicking Nitrogenase
    MOLECULES , 16 (1) pp. 442-465 (2011)
    doi: 10.3390/molecules16010442
  • Cossio P., Laio A., Pietrucci F.
    Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 13 (22) pp. 10421-10425 (2011)
    doi: 10.1039/c0cp02675a
  • Liu L., Laio A., Michaelides A.
    Initial stages of salt crystal dissolution determined with ab initio molecular dynamics
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 13 (29) pp. 13162-13166 (2011)
    doi: 10.1039/c1cp21077g
  • Tubiana L., Orlandini E., Micheletti C.
    Probing the Entanglement and Locating Knots in Ring Polymers: A Comparative Study of Different Arc Closure Schemes
    PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT , (191) pp. 192-204 (2011)