\
Physics and Chemistry of Biological systems
Alumni of the Molecular and Statistical Biophysics Group
Nicola Calonaci
Thesis pdf
List of Papers
Grad. Year: 2020
Supervisor: G. Bussi
Thesis Title: Computational investigations of structure probing experiments for RNA structure prediction
First Position after PhD: Insegnante scuola superiore
Giulia Amici
Thesis pdf
List of Papers
Grad. Year: 2020
Supervisor: C. Micheletti
Thesis Title: Statics and dynamics of physical linking: from confined polymers to chromatin filaments
First Position after PhD: Postdoc presso l'École normale supérieure di Parigi, Francia
Elena Tea Russo
Thesis pdf
List of Papers
Grad. Year: 2020
Supervisor: A. Laio
Thesis Title: Unsupervised protein family classification by Density Peak clustering
First Position after PhD: Insegnante scuola superiore e co.co.co presso la SISSA
Giulia Sormani
Thesis pdf
List of Papers
Grad. Year: 2020
Supervisor: A. Laio
Thesis Title: An unsupervised approach to the analysis of free energy landscapes and to protein design
First Position after PhD: Postdoc presso ICTP, Trieste
Francesca Cuturello
Thesis pdf
List of Papers
Grad. Year: 2019
Supervisor: G. Bussi
Thesis Title: Covariance models for RNA structure prediction
First Position after PhD: post-doc, area science park, Trieste
Andrea Cesari
Thesis pdf
List of Papers
Grad. Year: 2018
Supervisor: G. Bussi
Thesis Title: Enforcing ensemble averages in molecular
dynamics simulations using the Maximum
Entropy principle
First Position after PhD: Price Analyst @ Allianz SE
Nina Ilieva
Thesis pdf
List of Papers
Grad. Year: 2018
Supervisor: A. Laio
Thesis Title: Computational Analysis of Single
Molecule Force Spectroscopy Experiments
on Native Membranes
First Position after PhD: Laboratory technician @ CIC biomaGUNE, San-Sebastian/Donostia, Spain
Mattia Marenda
Thesis pdf
List of Papers
Grad. Year: 2018
Supervisor: C. Micheletti
Thesis Title: Topological Sorting and self-assembly of knotted molecules: models and simulations
First Position after PhD: MRC/UoE Cross Disciplinary Post-Doctoral Fellow @ Institute of Genetics and Molecular Medicine at the University of Edinburgh
Matteo Adorisio
Thesis pdf
List of Papers
Grad. Year: 2018
Supervisor: A. Celani
Thesis Title: Search, navigation and foraging: an optimal decision-making perspective
First Position after PhD: Insegnante scuola superiore
Antonio Suma
Thesis pdf
list
List of Papers
Grad. Year: 2017
Supervisor: C. Micheletti
Thesis Title: Static and dynamic properties of knotted
biopolymers: from bulk to nanochannels
and nanopores
First Position after PhD: Post-doc @ Institute for Computational Molecular Science, College of Science and Technology, Temple University, Philadelphia (USA)
Suma A., Di Stefano M., Micheletti C. Electric-Field-Driven Trapping of Polyelectrolytes in Needle-like Backfolded States MACROMOLECULES, 51 (12) pp. 4462-4470 (2018) doi: 10.1021/acs.macromol.8b00019
Cugliandolo L., Digregorio P., Gonnella G., Suma A. Phase Coexistence in Two-Dimensional Passive and Active Dumbbell Systems PHYSICAL REVIEW LETTERS, 119 (26) (2017) doi: 10.1103/PhysRevLett.119.268002
Cagnetta F., Corberi F., Gonnella G., Suma A. Large Fluctuations and Dynamic Phase Transition in a System of Self-Propelled Particles PHYSICAL REVIEW LETTERS, 119 (15) (2017) doi: 10.1103/PhysRevLett.119.158002
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
Suma A., Micheletti C. Pore Translocation of DNA Chains with Physical Knots BIOPHYSICAL JOURNAL, 112 (3) (2017) doi: 10.1016/j.bpj.2016.11.2546
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
Lorenzo Casalino
Thesis pdf
list
List of Papers
Grad. Year: 2017
Supervisor: A. Magistrato
Thesis Title: Pre-mRNA Splicing:
An Evolutionary Computational Journey
from Ribozymes to Spliceosome
First Position after PhD: Post-doc @ Department of Chemistry and Biochemistry, University of California, San Diego (USA)
Spinello A., Pavlin M., Casalino L., Magistrato A. A Dehydrogenase Dual Hydrogen Abstraction Mechanism Promotes Estrogen Biosynthesis: Can We Expand the Functional Annotation of the Aromatase Enzyme? CHEMISTRY-A EUROPEAN JOURNAL, 24 (42) pp. 10840-10849 (2018) doi: 10.1002/chem.201802025
Casalino L., Palermo G., Spinello A., Rothlisberger U., Magistrato A. All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115 (26) pp. 6584-6589 (2018) doi: 10.1073/pnas.1802963115
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
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
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
Elena Facco
Thesis pdf
list
List of Papers
Grad. Year: 2017
Supervisor: A. Laio
Thesis Title: The intrinsic dimension
of biological data landscapes
First Position after PhD: Big Data-Machine Learning Consultant @ MC Engineering
Negar Nahali
Thesis pdf
list
List of Papers
Grad. Year: 2017
Supervisor: A. Rosa
Thesis Title: Ring Polymers in Entangled
Solutions: Complex Structure and
Heterogeneous Dynamics
First Position after PhD: Post-doc @ Umeå University (Sweden)
Richard Cunha
Thesis pdf
list
List of Papers
Grad. Year: 2017
Supervisor: G. Bussi
Thesis Title: Dissecting Mg2+-RNA interactions using atomistic molecular dynamics
First Position after PhD: Post-doc @ University of Zurich (UZH) - Zurich, Switzerland
Sponer J., Bussi G., Krepl M., Banás P., Bottaro S., Cunha R., Gil-Ley A., Pinamonti G., Poblete P., Jurecka P., Walter N., Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview Chemical reviews 118 (8), 4177-4338 (2018) doi: 10.1021/acs.chemrev.7b00427
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
Luca Ponzoni
Thesis pdf
list
List of Papers
Grad. Year: 2016
Supervisor: C. Micheletti
Thesis Title: Knowledge-based identification of functional domains in proteins
First Position after PhD: Post-Doc @ University of Pittsburgh - USA
Paladino A., Marchetti F., Ponzoni L., Colombo G. The Interplay between Structural Stability and Plasticity Determines Mutation Profiles and Chaperone Dependence in Protein Kinases JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14 (2) pp. 1059-1070 (2018) doi: 10.1021/acs.jctc.7b00997
Granata D., Ponzoni L., Micheletti C., Carnevale V. Patterns of coevolving amino acids unveil structural and dynamical domains PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114 (50) (2017) doi: 10.1073/pnas.1712021114
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
Ponzoni L., Polles G., Carnevale V., Micheletti C. Spectrus: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets BIOPHYSICAL JOURNAL, 110 (3) (2016) doi: 10.1016/j.bpj.2015.11.355
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
Braida D., Donzelli A., Martucci R., Ponzoni L., Pauletti A., Langus A., Sala M. Mice discriminate between stationary and moving 2D shapes: Application to the object recognition task to increase attention BEHAVIOURAL BRAIN RESEARCH, 242 pp. 95-101 (2013) doi: 10.1016/j.bbr.2012.12.040
Giovanni Pinamonti
Thesis pdf
list
List of Papers
Grad. Year: 2016
Supervisor: G. Bussi
Thesis Title: Studying the dynamical properties of small RNA molecules with computational techniques
First Position after PhD: Post-Doc @ Freie Universität Berlin - Germany
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
Pinamonti G., Bottaro S., Micheletti C., Bussi G. RNA Conformational Fluctuations from Elastic Network Models: A Comparison with Molecular Dynamics and Shape Experiments BIOPHYSICAL JOURNAL, 110 (3) (2016) doi: 10.1016/j.bpj.2015.11.1772
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
Francesca Rizzato
Thesis pdf
list
List of Papers
Grad. Year: 2016
Supervisor: A. Laio
Thesis Title: Towards a deeper understanding of protein sequence evolution
First Position after PhD: Post-Doc @ Ecole Normale Superieure - Paris - France
Alejandro Gil Ley
Thesis pdf
list
List of Papers
Grad. Year: 2016
Supervisor: G. Bussi
Thesis Title: Enhanced sampling and force field corrections for RNA oligomers
First Position after PhD: Post-Doc @ University of Iowa - USA
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
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
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
Gil-Ley A., Bottaro S., Bussi G. RNA Conformational Ensembles: Narrowing the GAP between Experiments and Simulations with Metadynamics BIOPHYSICAL JOURNAL, 110 (3) (2016) doi: 10.1016/j.bpj.2015.11.2796
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
Andrea Perez-Villa
Thesis pdf
list
List of Papers
Grad. Year: 2015
Supervisor: G. Bussi
Thesis Title: Translocation of NS3 from Hepatitis C Virus on RNA: Insights from Atomistic Molecular Simulations
First Position after PhD: Post-Doc @ UPMC - Sorbonne Universities - Francia
Perez-Villa A., Darvas M., Bussi G. ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations (vol 43, pg 8725, 2015) NUCLEIC ACIDS RESEARCH, 44 (6) pp. 2975-2975 (2016) doi: 10.1093/nar/gkv1378
Perez-Villa A., Darvas M., Bussi G. ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations NUCLEIC ACIDS RESEARCH, 43 (18) pp. 8725-8734 (2015) doi: 10.1093/nar/gkv872
Ferrarotti M., 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
Edoardo Sarti
Thesis pdf
list
List of Papers
Grad. Year: 2015
Supervisor: A. Laio
Thesis Title: Assessing the structure of proteins and protein complexes through physical and statistical approaches
First Position after PhD: Post-Doc @ NIH (NINDS, National Institute of Neurological Diseases and Stroke), Bethesda USA
Battisti A., Zamuner S., Sarti E., Laio A. Toward a unified scoring function for native state discrimination and drug-binding pocket recognition PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 20 (25) pp. 17148-17155 (2018) doi: 10.1039/c7cp08170g 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 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 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
Guido Polles
Thesis pdf
list
List of Papers
Grad. Year: 2015
Supervisor: C. Micheletti
Thesis Title: Coarse-grained models for self-assembling systems
First Position after PhD: Research associate @ University of Southern California - USA
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
Ponzoni L., Polles G., Carnevale V., Micheletti C. Spectrus: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets BIOPHYSICAL JOURNAL, 110 (3) (2016) doi: 10.1016/j.bpj.2015.11.355
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
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
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
Zonta F., Polles G., Sanasi M., Bortolozzi M., Mammano F. The 3.5 angstrom X-ray structure of the human connexin26 gap junction channel is unlikely that of a fully open channel CELL COMMUNICATION AND SIGNALING, 11 (2013) doi: 10.1186/1478-811X-11-15
Francesca Mancini
Thesis pdf
list
List of Papers
Grad. Year: 2015
Supervisor: M. Marsili
A. Walczak
Thesis Title: Information theory in biochemical regulatory networks: a theoretical study
First Position after PhD: Risk Modeling & Analytics Specialist @ UBS - Switzerland
Ina Bisha
Thesis pdf
List of Papers
Grad. Year: 2014
Supervisor: A. Laio, A. Magistrato
Thesis Title: Atomistic Study of Structural and Functional Properties of Membrane Proteins
First Position after PhD: Post-Doc @ LMU/TUM - Munchen - Germany
Francesco Di Palma
Thesis pdf
List of Papers
Grad. Year: 2014
Supervisor: G. Bussi
Thesis Title: Conformational changes in the adenine riboswitch
First Position after PhD: Post-Doc @ Dipartimento di Fisica - Università Roma "La Sapienza" - Italy
Marco Di Stefano
Thesis pdf
List of Papers
Grad. Year: 2014
Supervisor: C. Micheletti, A. Rosa
Thesis Title: Structure and dynamics of entangled biopolymers: from knotted DNA to chromosomes
First Position after PhD: Post-Doc @ Centro Nacional de Analisis Genomico (CNAG) - Barcellona - Spain
Giuseppe Facchetti
Thesis pdf
List of Papers
Grad. Year: 2013
Supervisor: C. Altafini
Thesis Title: Computational approaches to complex biological networks
First Position after PhD: Post-Doc @ Börries and Hauke Group University of Freiburg, Germany
Gianpaolo Gobbo
Thesis pdf
List of Papers
Grad. Year: 2013
Supervisor: A. Laio
Thesis Title: Novel Approaches for an
Unprejudiced Characterization of
Rare Events
First Position after PhD: Postdoc @ B. J. Leimkuhler Group, School of Mathematics, University of Edinburgh, UK
Luca Ianeselli
Thesis pdf
List of Papers
Grad. Year: 2013
Supervisor: A. Laio; L. Casalis
Thesis Title: Development of a Miniaturized Electro-Fluidic Detector for Medical Diagnostics
First Position after PhD: Post-Doc @ Elettra Sincrotrone Trieste - Italy
Daniele Granata
Thesis pdf
List of Papers
Grad. Year: 2013
Supervisor: A. Laio, M. Vendruscolo
Thesis Title: Characterizing structure and free energy landscape of proteins by NMR-guided metadynamics.
First Position after PhD: Post-Doc @ ICMS, Temple University, Philadelphia, Pennsylvania, US
Duvan Franco Marin
Thesis pdf
List of Papers
Grad. Year: 2013
Supervisor: A. Magistrato
Thesis Title: Computational studies on DNA Damage Recognition
First Position after PhD: Customer service executive @ Booking.com.
Luca Tubiana
Thesis pdf
List of Papers
Grad. Year: 2012
Supervisor: C. Micheletti
Thesis Title: Equilibrium and kinetic properties of knotted ring polymers: a computational approach
First Position after PhD: R. Podgornik's group, University of Ljubljana, Slovenia
Zhaleh Ghaemi Bafghi
Thesis pdf
List of Papers
Grad. Year: 2012
Supervisor: A. Laio, P. Carloni
Thesis Title: Atomistic Simulation Studies of the Permeation Pharmacologicallly Relevant Molecules Through Lipid Membranes
First Position after PhD: Postdoc, Luthey-Schulten Group, University of Illinois, Urbana-Champaign, US
Nhu Trang Do
Thesis pdf
List of Papers
Grad. Year: 2012
Supervisor: G. Bussi, P. Carloni
Thesis Title: Investigating Peptide/RNA binding in Anti-HIV research by molecular simulations: electrostatic recognition and accelerated sampling
First Position after PhD: Postdoc, Karttunen's group, University of Waterloo, Waterloo, Canada
Fahimeh Baftizadeh
Thesis pdf
List of Papers
Grad. Year: 2012
Supervisor: A. Laio
Thesis Title: Atomistic Simulations of Short Peptides Aggregation by Advanced Computational Techniques
First Position after PhD: Postdoc, Trout's group, MIT, Boston, Massachusetts, US
Gianpaolo Chiriano
Thesis pdf
List of Papers
Grad. Year: 2011
Supervisor: G.Legname, M.L.Bolognesi, M.Roberti, A.Cavalli, P.Carloni
Thesis Title: Computer- and synthesis-based approaches towards the discovery of novel BACE-1 inhibitors as potential anti-Alzheimer’s drugs
First Position after PhD: Research assistant, University of Geneva, Switzerland
Salvatore Borganzone
Thesis pdf
List of Papers
Grad. Year: 2011
Supervisor: P. Carloni, G. Legname, M.L. Bolognesi
Thesis Title: Design, synthesis and molecular modeling studies of drug candidate compounds against prion diseases
First Position after PhD: Postdoc, Institute for Research in Biomedicine, Barcelona, Spain
Pilar Cossio
Thesis pdf
List of Papers
Grad. Year: 2011
Supervisor: A. Laio
Thesis Title: Protein physics by advanced computational techniques: conformational sampling and folded state discrimination
First Position after PhD: Postdoc, Hummer's Group, MPI, Frankfurt, Germany
Alessandro Bosco
Thesis pdf
List of Papers
Grad. Year: 2011
Supervisor: C. Micheletti, A. De Simone
Thesis Title: Mechanical response of ssDNA filaments and ss/dsDNA patches: experiments and simulations
First Position after PhD: Postdoc, L. Casalis' group, Elettra, Trieste, Italy
Raffaelo Potestio
Thesis pdf
List of Papers
Grad. Year: 2010
Supervisor: C. Micheletti
Thesis Title: Coarse-grained modelling of protein structure and internal dynamics: comparative methods and applications
First Position after PhD: Max Plank Institute for Polymer Research, Mainz, Germany
Roberto Marchese
Thesis pdf
List of Papers
Grad. Year: 2010
Supervisor:
Thesis Title:
Mauro Melli
Thesis pdf
List of Papers
Grad. Year: 2010
Supervisor: G. Scoles, M. Lazzarino
Thesis Title: Mechanical resonating devices and their applications in biomolecular studies
First Position after PhD: TASC, Trieste, Italy
Subhra Mandal
Thesis pdf
List of Papers
Grad. Year: 2010
Supervisor: G. Scoles, S. Krol
Thesis Title: Polyelectrolyte based NANO-approaches for Cancer therapy or diagnostics
First Position after PhD: Dept. TumorImmunology NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen,The Netherlands
Barbara Sanavio
Thesis pdf
List of Papers
Grad. Year: 2010
Supervisor: G. Scoles, L. Casalis
Thesis Title: Oriented Immobilization of Prion Protein
Demonstrated via Precise Interfacial Nanostructure Measurements
First Position after PhD: Elettra, Trieste, Italy
