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ELENCO DELLE ATTIVITA’ E DEI TITOLI DEL CANDIDATO VALUTABILI AI SENSI DEGLI ARTT. 10, 11, 12 E 13 DEL BANDO,

con Curriculum Vitae

di Mario Nicodemi

REDATTI AI SENSI DEGLI ARTT. 18, 38, 46 e 47 del D.P.R. n. 445/2000 (DICHIARAZIONI SOSTITUTIVE DI CERTIFICAZIONI E DELL’ATTO DI NOTORIETA’) Nota: poiché il regolamento di ateneo prevede la possibile presenza di commissari stranieri per la valutazione dei candidati, il testo è scritto anche in inglese. Per facilitarne la lettura, l’elenco delle attività e dei titoli è inserito anche nel CV e viceversa.

NAME AND AFFILIATION (NOME E AFFILIAZIONE)

Name (Nome e Cognome): MARIO NICODEMI Born (Nato): il 30/7/1968 a Napoli Citizenship (Cittadinanza): Italiana Current Position (Posizione attuale): Professore Associato di Fisica Teorica Settore Concorsuale (SC) 02/A2 Settore Scientifico Disciplinare (SSD) FIS/02 Affiliation (Affiliazione): Dipartimento di Fisica E. Pancini, Università di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia, 80126 Napoli, Italia Tel: 081-676475 / 3338995996 Email: Mario.Nicodemi@na.infn.it National Scientific Abilitation (ASN) to Full Professor obtained in SC 02/A2 and 02/B2 in 2013. I passed all the ASN thresholds with indicators up to 300% larger than the ASN official medians of the SC scientific sector. Abilitazione Scientifica Nazionale (ASN) conseguita nel 2013 per la I fascia nei Settori Concorsuali (SC) 02/A2 e 02/B2, superando tutte le mediane con indicatori fino al 300% superiori alle soglie di settore.

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SHORT SUMMARY OF MY CV (BREVE RIASSUNTO DEL CV)

Career summary - After my PhD in Theoretical Physics (1996), I worked as a postdoc at the École Supérieure de Physique et Chimie in Paris and Imperial College London. In 2000 I became Ricercatore (Research Scientist/Lecturer) at the University of Naples “Federico II”. In 2006 I was offered a position as Associate Professor at the then starting Complexity Science Centre at the University of Warwick, UK. In 2011 became Professore Associato in Theoretical Physics at the Univ. “Federico II”. In 2013 I got the National Scientific Abilitation (ASN) to Full Professor (SC 02/A2 and 02/B2). In 2015 I have been appointed National Coordinator of the INFN IS-BioPhys Research Initiative on Theoretical Physics and Biology, comprising ten teams in Italy. I am also member of the NIH The 4D Nucleome Consortium in the USA, and of the Berlin Institute of Health (BIH) in Germany. I serve in international panels for the management of research and its resources, including the Agence Nationale de la Recherce (ANR) in France, and in the boards of the journals EPJP and FPB. In 2016 I was the recipient of the Einstein BIH Fellowship Award by the Einstein Foundation, with B. Kobilka, the 2012 Nobel Prize for Chemistry, and I am the Einstein BIH Visiting Professor at MDC-Berlin.

Scientific activities - My research group works in Theoretical Physics on the Statistical Mechanics of Complex Systems and its applications to Molecular Biology. In particular, we contributed to the investigation of the structure of equilibrium and off-equilibrium processes in physical systems such as granular media and glassy materials, and to the understanding of the molecular mechanisms underlying the complex three-dimensional structure of the human genome and its links with gene regulation, by combining physics models, mathematical methods, computer simulations, high-throughput data analysis and technological developments. I published around 130 scientific papers with 3500 citations (h-index=34, Google Scholar). I got a number of invitations to international institutions and conferences worldwide (from LMB-MRC Cambridge, to Harvard in Boston, ANU in Canberra, Yukawa Inst. in Kyoto), including about 30 talks in the last 5 years.

In particular, I developed the Statistical Mechanics of non-thermal systems such as granular matter (see, e.g., Nature Materials 4, 121 (2005); Phys. Rev. Lett. 97, 158001 (2006)) where I discovered the presence of generalized Fluctuation-Dissipation Relations (Phys. Rev. Lett. 82, 3734 (1999)), the off-equilibrium nature of their relaxation (Phys.Rev.Lett. 79, 1575 (1997)), jamming phenomena (Phys. Rev. Lett. 100, 078001 (2008)), shear instabilities (Phys. Rev. Lett. 94, 188001 (2005)) and explained the anomalies of stress distribution (Phys. Rev. Lett. 80, 1340 (1998)). In the physics of glassy systems, we introduced the first fully solvable models for the glass/glass transition in spin-glasses and attractive colloids (Phys. Rev. Lett. 93, 215701 (2004)). We also discovered that vortex anomalous creep in superconductors at small temperatures, previously interpreted as “macroscopic quantum tunnelling”, is a “classical” off-equilibrium phenomenon (Phys. Rev. Lett. 86, 4378 (2001)).

I pioneered the development of polymer physics to model and predict the 3D organization of chromosomes in the nucleus of cells and its functional implications (see, e.g., PNAS 109, 16173 (2012); Nature Sci. Rep. 6, 29775 (2016)). We are now using polymer physics to develop novel diagnostic tools for diseases linked to chromosome mis-folding, such as

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congenital disorders and cancer. In particular, I discovered that chromosomes have a hierarchical 3D structure deeply linked to gene regulation (Mol. Sys. Bio. 11, 852 (2015)). I also discovered some of the molecular mechanisms that shape folding, specifically that active Pol-II (S2p) and PRC2 (Ezh2) respectively mediate homotypic interactions between active and poised genes in the case study of the HoxB region in mouse embryonic stem cells (Nature Struct. Mol. Bio. in press (2017)). I also proposed the first molecular theory to explain symmetry breaking at X-Chromosome Inactivation (Phys. Rev. Lett. 98, 108104 (2007) and N&V Nature Physics 3, 221 (2007)) and investigated the mechanisms underlying pattern formation in cell development (Phys. Rev. Lett. 108, 158103 (2012)). I introduced stochastic models to dissect the network of single-cell states traversed during cell transformations and discovered novel states in cell differentiation and reprogramming (Nature Sci. Rep. 4, 3692 (2014); Gen. Bio. 17, 103 (2016)). We have also developed and patented GAM, a new technology to map chromatin interactions genome wide (Nature doi:10.1038/nature21411 (2017)), which is expanding our understanding of the complexity of gene regulation and its link to the 3D structure of the genome.

Teaching activities - I have been teaching Physics courses in different countries since more than 15 years, supervising a number of students and Post-Docs (approx. 30 in the last 10 years). I now lecture a Statistical Mechanics course on Complex Systems and a Bioinformatics course at the Physics Master and PhD level. I also teach the mechanics and thermodynamics basic course (Fisica Generale I) to the BSc level (Laurea Triennale) in Engineering and in Informatics. I served in different boards of university teaching programs (e.g., BSc, MSc, PhD in IT, UK, etc.) and in international science and teaching schools. I also took part in science popularization events such as Futuro Remoto, Città della Scienza and DNA in Sound. In 2016, for instance, I have been invited to give a TEDxCNR Talk and TV interviews on my research activities at RAI News.

Management, administration and funding - I have participated or lead a number of international research teams and consortia in IT, UK, UE, USA, with co-authors at EPSCI-Paris, IC-London, EBI-Cambridge, ETHZ, MDC-Berlin, UCSF, MIT, McGill-Canada, etc. I organized a dozen international conferences. And I seat in the editorial boards of the European Physics Journal and of Frontiers in Biophysics. I have taken part in a number of departmental and university administration activities and committees. I also serve in international panels for the management of research and its resources, including the Agence Nationale de la Recherce (ANR) CE12 of the French Ministry of Research. I act as a reviewer for funding agencies for a variety of countries (e.g., NSF-USA, EPSRC-UK, ANR-FR, MIUR-IT, etc.). I have been awarded a number of grants for research, high-performance computing and infrastructures from IT, UK, DE, EU and USA institutions, including in the last couple of years two CINECA ISCRA grants for supercomputing, an USA NIH grant on 4D Nucleome Research and a German grant from the Einstein Foundation.

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Curriculum Vitae di Mario Nicodemi

CAREER SUMMARY (RIASSUNTO CARRIERA)

Present 2017- Einstein BIH Visiting Professor, Max Delbrück Centre, Berlin, DE 2015- National Coordinator of INFN Research Initiative IS-Theoretical BioPhys, IT 2011- Associate Professor of Theoretical Physics, Univ. of Naples Federico II, IT 2005- Coordinator of the Naples Unit of INFN IS-Theor. BioPhys, IT

Past 2012-2015 Coordinator of Supercomputing Resources of INFN IS-Theor. BioPhys, IT 2006-2010 Associate Professor, Complexity DTC & Physics Dept., Univ. of Warwick, UK 2000-2011 Ricercatore (Research Scientist/Lecturer), Univ. of Naples Federico II, IT 1999-2000 Associate Researcher, Math. Dept., Imperial College, London, UK

Supervisor: Prof. H.J. Jensen 1996-1999 Della Riccia Junior Research Fellow and INFM PostDoc, ESPCI/UniNa

Supervisor: Prof. H.J. Herrmann/A. Coniglio

EDUCATION (FORMAZIONE)

1996 PhD in Physics, University of Naples Federico II, IT Supervisor: Prof. A. Coniglio

1992 Laurea cum Laude in Physics, University of Naples Federico II, IT Supervisor: Prof. A. Coniglio

MAIN FELLOWSHIPS, HONOURS AND AWARDS (CONSEGUIMENTO DI PREMI, RICONOSCIMENTI E PARTECIPAZIONI A ENTI DI RICERCA)

2016 Einstein BIH Fellowship Award, Einstein Foundation, Berlin, DE 2015- Member of the NIH 4D Nucleome Consortium, USA 2010- Research Associate to CNR (Italian National Research Council), SPIN, IT 2006-10 Member of the Institute of Physics, UK 2005-2006 Visiting Fellowship, Australian National University, Canberra, Australia 2005 Visiting Fellowship, Kavli Institute for Theoretical Physics, UCSB, USA 2004 Visiting Fellowship, Institute Henri Poincaré, Paris, FR 2000-2006 Research Associate to INFM (Instituto Nazionale Fisica della Materia), IT 2000- Research Associate to INFN (Instituto Nazionale Fisica Nucleare), IT 1996-1999 Della Riccia Research Fellowship Award 1993-1996 PhD Studentship Award, MIUR - University of Naples Federico II

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TEACHING, COACHING AND OUTREACH ACTIVITIES (ATTIVITÀ DIDATTICA, DI DIDATTICA INTEGRATIVA E DI SERVIZIO AGLI STUDENTI)

I have been teaching Physics courses for more than 15 years, in different countries. I supervised a number of students, PhDs and Post-Docs (approx. 30 in the last 10 years), most of them having today top jobs in business and science. Currently, I coordinate a research group of 8 people. I have served in the board of a number of teaching programs and committees (e.g., BSc, MSc, PhD in Physics and Bioinformatics, in IT, UK, etc.) and international training projects (see lists below), such as the “XIX SIBPA School of Pure and Applied Biophysics” (Venice, 2015). I have also contributed to science popularization events, such as Futuro Remoto, Città della Scienza and DNA in Sound. In 2016 I was invited to give a public speech in the celebrated series of TEDx Talks, in an event organized by RAI and CNR. In 2017 I have been invited for an interview at RAI News about my research activities.

Main lectured courses (Elenco principali corsi tenuti) At the University of Naples Federico II, in particular, I currently teach undergraduate and graduate courses for the Lauree in Fisica, in Informatica and Ingegneria Informatica, receiving excellent scores from the students. The list of main courses I lectured, in Naples and elsewhere, includes: 1) 2012-17, "Fisica Generale I", Laurea Triennale in Informatica, Univ. Napoli Federico II.

2) 2012-17, "Fisica Generale I", Triennale in Ingegneria Informatica, Univ. di Napoli

Federico II.

3) 2004-17, "Sistemi Complessi", Laurea Magistrale in Fisica, Univ. di Napoli Federico II.

4) 2009-17, "Bioinformatica", Laurea Magistrale in Informatica, Univ. Napoli Federico II.

5) 2007-10, "Self-Organization & Emergence", Doctorate in Complexity, Univ. of

Warwick, UK.

6) 2008-10, "Physics of Fluids", Dept. of Physics, Univ. of Warwick, UK.

7) 2002-09, "Meccanica Statistica e Informatica", Informatica, Univ. di Napoli Federico II.

8) 2003-07, "Abilità Informatiche", Facoltà di Giurisprudenza, Univ. di Napoli Federico II.

9) 2001-02, "Fisica Generale", Facoltà di Farmacia, Univ. di Napoli Federico II.

10) 1997-99, "Fisica Generale", Biologia, Università del Sannio, Benevento.

I was also in charge of the following tutoring courses with practical exercises for the students:

1) 2001-05, Esercitazioni di "Fisica Generale", Laurea in Fisica, Univ. Napoli Federico II. 2) 1999-00, Esercitazioni "Metodi Matematici", Math Dept., Imperial College, London.

Organization of international training schools (Elenco principali scuole internazionali organizzate)

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I organized several scientific events aimed at training students, PhD and postdocs (see below the list of organized conferences and workshops), including in the last couple of years the XIX SIBPA School of Pure and Applied Biophysics in Venice in 2015. Supervised students, PhD and postdocs in the last 10 years (Elenco tesi di studenti, PhD e postdoc seguiti come relatore negli ultimi 10 anni) I supervised a number of undergraduates, graduates, PhD students, and postdocs. For brevity, the following list includes 30 of the students I supervised in the last ten years: Silvio Romano, Luca Fiorillo, Carlo Annunziatella, Mariano Barbieri, Simona Bianco, Andrea Chiariello, Andrea Esposito, Pasquale Franzese, Andrea Piccolo, Sergio Sarnataro, Giovanni Terzo, Giovanni Laudanno, Emanuele Varriale, Federica Gucci, Fabio Salvati, Anna Longobardi, Anas Rana, Emanuela de Falco, Ciro di Lanno, Gaetano Pellegrino, Jon Armond, Denis Grebenkov, Dan Barker, Melania Barile, Paolo Casale, Polly Downton, Antonio Scialdone, Valentino Bianco, Sam Brand, Ilaria Cataudella, Deborah Pallotti, … Main popularization events for a broader public (Elenco eventi di divulgazione scientifica e terza missione) I have taken part in several events of popularization of science aimed at a broader public. Here is a list of those in the last few years: 1) 2017 Talk at Città della Scienza, on the Physics-Biology frontier, Napoli

2) 2017 Interview on the physics of DNA with RAI News.

3) 2016 TEDxCNR “Why our DNA is not like a spaghetti dish”, Roma

4) 2016 Per una formazione in tempo di crisi, presso Editoriale Scientifica, Napoli

5) 2016 Disseminazioni, PuntoOrg, Napoli

6) 2016 Vita e Natura: una visione sistemica, Istituto Italiano Studi Filosofici, Napoli

7) 2015 Economia, Scienza, Musica, Univ. Ca’ Foscari, Venezia

8) 2011 DNA in Suono, IGB Napoli

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OUTLINE OF RESEARCH ACHIEVEMENTS (ATTIVITÀ DI RICERCA SCIENTIFICA)

My group works in Theoretical Physics on Statistical Mechanics of Complex Systems and on its applications to Molecular Biology, by combining statistical physics models, computer simulations, high-throughput data analysis and technological developments. I published around 130 scientific papers in international journals (see list below) with approximately 3500 citations (h-index=34, Google Scholar). I received a number of invitations to international institutions and conferences worldwide (from LMB-MRC Cambridge, to Harvard in Boston, ANU in Canberra, Yukawa Inst. in Kyoto), including about 30 talks in the last 5 years (see list below). Here is a summary of my research achievements. Statistical Mechanics of Complex Systems - I worked on equilibrium and off-equilibrium Statistical Mechanics of complex systems such as molecular glasses and spin glasses, vortices in superconductors, and in particular on granular media, by use of mathematical and computational approaches. My group has an international reputation in the field (see, e.g., my review in Nature Materials 4, 121 (2005)). I pioneered the development of the methods of Statistical Mechanics for granular media, helping to identifying the statistical distribution of micro-states of such non-thermal systems (the equivalent of Boltzmann distribution, Phys.Rev.Lett. 97, 158001 (2006)) and discovering, first, the existence of generalized Fluctuation-Dissipation Relations (Phys. Rev. Lett. 82, 3734 (1999)), now widely used in the community. I have identified the 'glassy' (off-equilibrium) nature of their dynamics (Phys. Rev. Lett. 79, 1575 (1997), Phys. Rev. Lett. 100, 078001 (2008)) and the presence of Kelvin-Helmholtz instabilities similar to those of usual fluids (Phys. Rev. Lett. 94, 188001 (2005)). I also investigated their stress anomalies (Phys. Rev. Lett. 80, 1340 (1998)) and the origin of size-segregation effects ('Brazil-nut effect', Phys. Rev. Lett. 95, 078001 (2005), Phys. Rev. Lett. 97, 038001 (2006)). In the physics of glassy systems, we introduced the first fully solvable models of the glass/glass transition in spin-glasses and attractive colloids (Phys. Rev. Lett. 93, 215701 (2004)); we also developed new Monte Carlo cluster algorithms for frustrated spin-systems (Phys. Rev. Lett. 72, 1541 (1994)). In the context of type-II superconductors, we discovered that the anomalous creep of magnetic vortices at small temperatures, previously interpreted as “macroscopic quantum tunnelling”, is a “classical” phenomenon of off-equilibrium relaxation (Phys.Rev.Lett. 86, 4378 (2001), Phys.Rev.Lett. 87, 259702 (2001)). We have also identified the structure of thermal fluctuations in an important class of correlated systems of Statistical Mechanics (Phys. Rev. Lett. 84, 3744 (2001)). Statistical Physics and Molecular Biology - New experimental advances in Molecular Biology are generating quantitative data on a genomic scale, the understanding of which requires the methods of Theoretical Physics. This field, known as Biological Physics, is an internationally strategic research area, having the potential to lead to important discoveries of basic science as well as revolutionary applications in biomedicine. In that context, I work within an international network of experimental collaborations. I have introduced the first molecular model explaining the symmetry breaking events occurring in X-Chromosome Inactivation, a chromosome wide regulatory process whereby only one of the two Xs in each female cell is inactivated (see, e.g., Phys.Rev.Lett. 98, 108104 (2007) and N&V Nature Physics 3, 221 (2007)). One of my current main research lines investigates the 3D organization of chromosomes in the cell nucleus and its functional implications. I pioneered the development of polymers physics to model and predict chromosome folding (see PNAS 109, 16173 (2012), Nature Sci. Rep. 6, 29775 (2016)). Our String&Binders Model is a reference model in the field, the first to explain and predict with high accuracy

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genome-wide experimental data (Hi-C, GAM and FISH) on chromosome interactions, across cell types. Our discoveries are opening the way to new diagnostic methods for diseases linked to chromosome mis-folding, such as congenital disorders and cancer. In particular, we discovered some of the key mechanisms underlying the formation of TADs, genomic regions with enriched functional interactions (see our review in Curr. Op. Cell Bio. 28, 90 (2014)). By combining polymer physics, bioinformatics and experimental chromosome contact maps, with A. Pombo in Berlin, J. Dostie at McGill and C. Semple in Edinburgh, we discovered the hierarchical nature of the spatial organization of the mammalian genome, showing that chromosomes are folded in a domain-within-domain structure (metaTADs) whose reorganization during embryonic differentiation is functionally linked to the control of gene activation (Mol. Sys. Bio. 11, 852 (2015)). With Ana Pombo we have also developed and patented GAM a ligation-free technology to map genome-wide chromosome interactions, beyond pairwise contacts, alternative to 3C based methods (Nature doi:10.1038/nature21411 (2017)). With GAM we discovered, for instance, that highly transcribed regions or super-enhancers tend to form three-way or multiple contacts, expanding the understanding of the complexity of gene regulation and its link to the 3D structure of the genome. By combining modelling and experiments in the case study of the HoxB region in mouse embryonic stem cells, we discovered some of the molecular mechanisms that shape folding and shown that gene activation states plays a key role (Nature Struct. Mol. Bio. in press (2017)): we found that physical contacts occur separately between active and poised genes, and that their homotypic interactions are mediated by active Poll-II (S2p) and PRC2 (Ezh2) molecules respectively, which can explain the observed folding patterns. We are also investigating the nature of cell differentiation and reprogramming, and, in particular, the related events of spontaneous pattern formation (Phys. Rev. Lett. 108, 158103 (2012)). By using the mathematical techniques of stochastic processes, with S. Teichmann in Cambridge and R. Jaenisch at MIT, we have introduced a model to describe the complex dynamics of cell transformations, leading to the first quantitative identification of the network of single-cell states traversed during T-cell differentiation (Gen. Bio. 17, 103 (2016)) and mouse fibroblast reprogramming (Nature Sci. Rep. 4, 3692 (2014)).

PATENTS (TITOLARITÀ DI BREVETTI)

With the Max Delbruck Centre in Berlin, in 2014 we filed a European Patent (EPO n.3031929) now extended to an International Patent (PCT/EP2015/079413) on a new technology, Genome Architecture Mapping (GAM), to map genome-wide chromosome physical contacts in the cell nucleus, based on the statistical reconstruction of interaction frequencies of sequenced genomic regions extracted from 100nm wide nuclear sections.

MAIN AWARDED GRANTS AND FUNDING (CAPACITÀ DI ATTRARRE FINANZIAMENTI COMPETITIVI)

I have been awarded as Principal Investigator (PI) or team member a variety of grants for Scientific Research, Training, High Performance Computing and infrastructure development from EU, IT, DE, UK, USA funding agencies, including: 1) 2017-2020 Einstein BIH Visiting Professor Fellowship 2016 grant (DE), PI 2) 2016-2017, CINECA Supercomputing ISCRA- HP10CRTY8P, PI 3) 2015-2020, NIH, S.D. Center for 4D Nucleome Res. 1U54DK107977-01 (USA), PI

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4) 2015-2016, CINECA Supercomputing ISCRA-HP10CYFPS5, PI 5) 2013-2016, POR DIMO, Regional Research Funds, approved but not yet funded 6) 2009-2012, CASPUR Supercomputing, several annual projects, PI 7) 2005-2006, Galileo Project IT-FR, "Slow relaxations in granular media", PI 8) 2000-6, CINECA Supercomputing, several annual projects, PI 9) 2009-2012, PRIN-2009 (Progetti di Ricerca di Interesse Nazionale) 10) 2008, IAS, Warwick UK, "Analysis of Population Data for CVD Risk" 11) 2006, Ricerca Regione Campania, Legge 5, "Dynamics in complex systems" 12) 2004-06, PRIN-2004 13) 2003, EU Network, "Dynamical Arrested State of Soft Matter and Colloids" 14) 2002-04, PRIN-2002 15) 2002-04, FIRB-2002 16) 2000-02, PRIN-2000

MANAGEMENT AND ADMINISTRATION OF RESEARCH (ORGANIZZAZIONE, DIREZIONE E COORDINAMENTO DI CENTRI O GRUPPI DI RICERCA,

O PARTECIPAZIONE AGLI STESSI E ALTRE ATTIVITÀ)

In 2015 have been appointed National Coordinator of the INFN IS-BioPhys Research Initiative on Theoretical Physics and Biology, a consortium comprising ten research centres in Italy. And I am part of the INFN-GrIV National Supercomputing Initiative. I am also member of the NIH The 4D Nucleome Consortium in the USA, and of the Berlin Institute of Health (BIH) in Germany. I have participated or lead a number of international research teams and networks in EU, IT, UK, USA, including a variety of partners and co-authors, such as H.J. Herrmann now at ETHZ, H.J. Jensen Imperial College London, A. Coniglio Naples, R. Jaenisch MIT, B. Panning UCSF, A. Pombo MDC-Berlin, S. Teichmann EBI-Cambridge, S. Colin Edinburgh, J. Dostie McGill-Canada, etc. I act as reviewer for several research funding agencies, including NSF-USA, EPSRC-UK, ANR-FR, INSERM-FR, MIUR-IT, and for a number of journals including Nature and Science. Membership and Management of Research Institutions (Organizzazione, direzione, coordinamento o partecipazione in centri di ricerca) I am member of several research institutions and funding agencies, where I served in a number of steering committees and panels, including: 1) 2017-20 Einstein BIH Visiting Professor, MDC-Berlin, DE

2) 2015- National Coordinator of INFN Research Initiative IS-BioPhys, IT

3) 2015- Member of the USA NIH Consortium “The 4D Nucleome”

4) 2012-2015 Coordinator of Supercomputing Resources of INFN IS-BioPhys, IT

5) 2005- Coordinator of the Naples Unit of INFN Res. Init. IS-BioPhys, IT

6) 2010- Research Associate to CNR (Italian National Research Council)

7) 2006-2010 Member of IoP (UK Institute of Physics), UK

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8) 2000- Research Associate to INFN (Italian National Institute of Nuclear Physics)

9) 2000-2006 Research Associate to INFM (Italian National Institute of Matter Physics)

Editorial Board Memberships of Scientific Journals (Partecipazione a comitati editoriali di riviste scientifiche)

1) 2013- Frontiers in Physics and in Biophysics

2) 2011- European Physical Journal - P

3) 2005-2006 Journal of Physics: Condensed Matter

Organization of International Conferences (Organizzazione di conferenze di rilevanza internazionale) I have organized or co-organized 16 international conferences in Physics and on applications to Molecular Biology, funded by national and international institutions (EU, UK, IT, FR, AUS, …): "Unifying concepts in granular media and glasses" (Capri, 2003), "DygraM" (Rennes, 2006), "Granular Media" (Canberra, 2006), "Statics and dynamics of granular media and colloidal suspensions"(Naples, 2007), BioMEMS and Nanotechnology III (Canberra, 2007), "Patterns in Particle Systems" (Warwick, 2008), "Networks&Organiz. in cell biology" (UK, 2008), European Conf. on Complex Systems (UK, 2009), "Stat. Mech. of Molecular and Cell Biology" (UK, 2009), "Unwinding Complexity" (Brisbane, 2010), "Quantitative Methods in Gene Regulation" (IoP London, 2011), "Stat.Mech. in Systems Biology" (Capri, 2012), “Quantitative Methods in Gene Regulation II” (Cambridge/IoP 2013), “Critical Phenomena in Complex Systems" (Capri, 2014), “Interdisciplinary views on chromosome structure and function” (ICTP, 2014), “Biophys 2016” (Bari, 2016), “Interdisciplinary views on chromosome structure and function II” (ICTP, 2016).

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ADMINISTRATION AND ORGANIZATIONAL ACTIVITIES (ATTIVITÀ GESTIONALI, ORGANIZZATIVE E DI SERVIZIO)

I served in a number of committees and panels for organizational and administration activities at the Department and University levels, in Italy and abroad. In particular, I am member of the CE12 panel of the Agence Nationale de la Recherce (ANR) for the Ministry of Research in France. Departmental Administration and Organizational Activities (Attività gestionali, organizzative e di servizio di Dipartimento)

1) 2014 Member of the Commissione di Valutazione di accesso al Dottorato in

Fisica (Physics PhD Admission board), Univ. of Naples Federico II 2) 2013- Member of the Collegio di Dottorato in Fisica (Physics PhD board),

University of Naples Federico II 3) 2012 Member of a final PhD Panel at the Niels Bohr Institute,

Copenhagen, DK 4) 2009 Member of a final PhD Panel at the Dept. of Physics, University of

Leicester, UK 5) 2007-2010 Member of the board of the Doctorate in Complex Systems, University

of Warwick, UK 6) 2006-2016 Member of the Collegio di Dottorato in Biologia Computazionale e

Bioinformatica (Comput. Bio. & Bioinf. PhD board), Univ. Naples Fed.II 7) 2002-2006 Member of the Collegio di Dottorato in Fisica (Physics PhD board),

University of Naples Federico II Administration and Organization for Universities and for the Ministry of Research (Attività gestionali, organizzative e di servizio di Ateneo e del Ministero della Ricerca)

1) 2015-17 CE12 Panel Member of the French Ministry of Research funding agency Agence Nationale de la Recherche (ANR), FR

2) 2008 Member of the Commissione Finale di Dottorato in Sistemi Complessi (PhD in Complex Systems, Final Award board), University of Turin

3) 2004-2010 Elected member in the Consiglio di Facoltà di Scienze (Science Faculty Council), University of Naples Federico II

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LIST OF MAIN SCIENTIFIC PUBLICATIONS (ELENCO PRINCIPALI PUBBLICAZIONI SCIENTIFICHE)

P1. International journals Publications selected for the Evaluation Commission

(Pubblicazioni oggetto di valutazione specifica da parte della commissione)

1) R.A. Beagrie, A. Scialdone, M. Schueler, D.C.A. Kraemer, M. Chotalia, S.Q. Xie, M. Barbieri, I. de Santiago, L.-M. Lavitas, M.R. Branco, J. Fraser, J. Dostie, L. Game, N. Dillon, P.A.W. Edwards, M. Nicodemi*, A. Pombo*, “Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM), a novel ligation-free approach”, Nature, doi:10.1038/nature21411 (2017), published on-line 8/3/2017 and to appear in print 23/3/2017. (* joint last author)

2) A.M. Chiariello, S. Bianco, C. Annunziatella, A. Esposito, M. Nicodemi, “Polymer physics of chromosome large-scale 3D organisation”, Nature Scientific Reports 6, 29775 (2016).

3) J. Fraser, C. Ferrai, A.M. Chiariello, M. Schueler, T. Rito, G. Laudanno, M. Barbieri, B.L. Moore, D.C.A. Kraemer, S. Aitken, S.Q. Xie, K. Morris, M. Itoh, H. Kawaji, I. Jaeger, Y. Hayashizaki, P. Carninci, A.R.R. Forrest, FANTOM Consortium, C.A. Semple, J. Dostie, A. Pombo, and M. Nicodemi. “Hierarchical folding of chromosomes is linked to transcriptional changes in cellular differentiation”, Molecular System Biology 11, 852 (2015).

4) M. Barbieri, M. Chotalia, J. Fraser, L.-M. Lavitas, J. Dostie, A. Pombo, M. Nicodemi, “Complexity of chromatin folding is captured by the Strings & Binders Switch model”, P.N.A.S. U.S.A. 109, 16173 (2012).

5) D.S. Grebenkov, M. Pica Ciamarra, M. Nicodemi, and A. Coniglio, “Flow, ordering, and jamming of sheared granular suspensions”, Phys. Rev. Lett. 100, 078001 (2008).

6) M. Nicodemi and A. Prisco, “A Symmetry Breaking Model for X Chromosome Inactivation”, Phys. Rev. Lett. 98, 108104 (2007).

7) M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, “Thermodynamics and Statistical Mechanics of Dense Granular Media”, Phys. Rev. Lett. 97, 158001 (2006).

8) P. Richard, M. Nicodemi, R. Delannay, P. Ribière, D. Bideau, “Slow relaxation and compaction of granular systems”, Nature Materials 4, 121 (2005).

9) M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, “Shear instabilities in granular mixtures”, Phys. Rev. Lett. 94, 188001 (2005).

10) M. Nicodemi and H.J. Jensen, “Creep of superconducting vortices in the limit of vanishing temperature: A fingerprint of off-equilibrium dynamics”, Phys. Rev. Lett. 86, 4378 (2001).

11) M. Nicodemi, “Dynamical response functions in models of vibrated granular media”, Phys. Rev. Lett. 82, 3734 (1999).

12) M. Nicodemi, “Force correlations and arches formation in granular assemblies”, Phys. Rev. Lett. 80, 1340 (1998).

My other international publications (Altre pubblicazioni internazionali)

13) M. Barbieri, S.Q. Xie, E. Torlai Triglia, A.M. Chiariello, S. Bianco, I. de Santiago, M.R. Branco, D. Rueda, M. Nicodemi*, A. Pombo*, “Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells”, Nature Struct. Mol. Bio, in press (2017). (* joint last author)

14) S. Bianco, A.M. Chiariello, C. Annunziatella, A. Esposito, M. Nicodemi, “Predicting chromatin architecture from models of polymer physics”, Chromosome Res., doi:10.1007/s10577-016-9545-5 (2017).

15) C. Annunziatella, A.M. Chiariello, S. Bianco, M. Nicodemi, “Polymer models of the hierarchical folding of the HoxB chromosomal locus”, Phys. Rev. E 94, 042402 (2016).

16) V. Proserpio, A. Piccolo, L. Haim-Vilmovsky, G. Kar, T. Lönnberg, V. Svensson, J. Pramanik, K. Natarajan, W. Zhai, X. Zhang, G. Donati, M. Kayikci, J. Kotar, A.N. Mckenzie, R. Montandon, O. Billker, S. Woodhouse, P. Cicuta, M. Nicodemi*, S.A. Teichmann*. “Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation”, Genome Biology 17, 103 (2016). (* joint last author)

17) A.M. Chiariello, S. Bianco, A. Piccolo, C. Annunziatella, M. Barbieri, A. Pombo and M. Nicodemi, “Polymer models of the organization of chromosomes in the nucleus of cells”, Mod. Phys. Letters B 29, 1530003 (2015).

18) M. Zamparo, F. Chianale, C. Tebaldi, M. Cosentino Lagomarsino, M. Nicodemi, A. Gamba, “Dynamic membrane patterning, signal localization and polarity in living cells”, Soft Matter 11, 838

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(2015). 19) J.W. Armond, K. Saha, A. Rana, C. Oates, R. Jaenisch, M. Nicodemi*, S. Mukherjee*, “A

stochastic model dissects cell states in biological transition”, Nature Scientific Reports 4, 3692 (2014). (* joint last author)

20) A.Pombo, M. Nicodemi, “Models of chromosome structure”, Current Opinion in Cell Biology 28, 90 (2014).

21) A. Pombo, M. Nicodemi, “Physical mechanisms behind the large scale features of chromatin organization”, Transcription 5, e28447 (2014).

22) F.P. Casale, G. Giurato, G. Nassa, J.W. Armond, C.J. Oates, D. Cora ́, A. Gamba, S. Mukherjee, A. Weisz, M. Nicodemi, “Single-Cell States in the Estrogen Response of Breast Cancer Cell Lines”, PLoS One 9, e88485 (2014).

23) M. Barbieri, A. Scialdone, A. Gamba, A. Pombo, M. Nicodemi, “Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cel nucleus”, Soft Matter 9, 8631 (2013). (Invited review)

24) M. Barbieri, M. Chotalia, J. Fraser, L.-M. Lavitas, J. Dostie, A. Pombo, M. Nicodemi, “A polymer model ex- plains the complexity of large-scale chromatin folding”, Nucleus 4; 4, 1-7 (2013). (Journal cover feature July/Aug. 2013)

25) M. Barbieri, A. Scialdone, A. Piccolo, A.M. Chiariello, C. di Lanno, A. Prisco, A. Pombo, M. Nicodemi, “Polymer models of chromatin organization”, Frontiers in Genetics: System Biology 4, 113 (2013).

26) M. Barbieri, M. Chotalia, J. Fraser, L.-M. Lavitas, J. Dostie, A. Pombo, M. Nicodemi, “A model of the large scale organization of chromatin”, Biochemical Society Transactions 41, 508 (2013).

27) A. Gamba, M. Nicodemi, J. Soriano, A. Ott, “Critical Behavior and Axis defining Symmetry Breaking in Hydra embryonic Development”, Phys. Rev. Lett. 108, 158103 (2012).

28) V. Bianco, A. Scialdone, M. Nicodemi, “Colocalization of Multiple DNA Loci: a Physical Mechanism”, Biophys. Jour. 103, 2223-2232 (2012).

29) D. Bureau,S.Brand,R.C.Ball,M.Nicodemi,“Flow regimes of a fluid driven granular suspension”, Granular Matter 14, 175 (2012).

30) A.Scialdone, M. Barbieri, D. Pallotti, M. Nicodemi, “Mean-Field Theory of the Symmetry Breaking Model for X Chromosome Inactivation”, Prog. Theor. Phys. Sup. 191, 40 (2011).

31) A.Scialdone, I. Cataudella, M. Barbieri, M. Nicodemi, “Conformation Regulation of the X Chromosome Inactivation Center: a Model”, PLoS Comp. Bio. 7, e1002229 (2011).

32) M. Pica Ciamarra, R. Pastore, M. Nicodemi, A. Coniglio, “Jamming phase diagram for frictional particles”, Phys. Rev. E 84, 041308 (2011).

33) S. Brand, R.C. Ball, M. Nicodemi, “Stochastic transitions and jamming in granular pipe flow”, Phys. Rev. E 83, 031309 (2011).

34) A. Scialdone, M. Nicodemi, “Diffusion based DNA-target Colocalization by Thermodynamic Mechanisms”, Development 137, 3877 (2010).

35) A.Scialdone, M. Nicodemi, “Passive DNA shuttling”, Europhys. Lett. 92, 20002 (2010). 36) M. Pica Ciamarra, M. Nicodemi, A. Coniglio, “Recent results on the jamming phase diagram”, Soft

Matter 6, 2871 (2010). 37) A.Scialdone, M. Nicodemi, “Statistical Mechanics models for X-Chromosome Inactivation”,

Advances In Complex Systems 13, 367 (2010). 38) S. Brand, M. Pica Ciamarra, M. Nicodemi, “Complex flow in granular media”, Advances In Complex

Systems 13, 339 (2010). 39) R. Amato, M. Pinelli, D. D’Andrea, G. Miele, M. Nicodemi, G. Raiconi, and S. Cocozza, “A novel

approach to simulate gene-environment interactions in complex diseases”, BMC-Bioinformatics 11, 8 (2010).

40) M. Nicodemi, M. Pica Ciamarra, A. Coniglio, “Rheology of sheared monodisperse granular suspensions”, Eur.Phys.Jour. Special Topics 179, 157 (2009).

41) E. Piegari, V. Cataudella, R. Di Maio, L. Milano, M. Nicodemi, and M.G. Soldovieri, “Electrical resistivity tomography and statistical analysis in landslide modelling: A conceptual approach”, Jour. of Applied Geophys. 68, 151 (2009).

42) M. Nicodemi, A. de Candia, A. Coniglio, “Aggregation of fibrils and plaques in amyloid molecular systems”, Phys. Rev. E 80, 041914 (2009).

43) A.Scialdone and M. Nicodemi, “DNA loci cross-talk through thermodynamics”, Journal of Biomedicine and Biotechnology, 516723 (2009)

44) A.Veglio, A. Gamba, M. Nicodemi, F. Bussolino, G. Serini, “A symmetry breaking mechanism for epithelial cell polarization” Phys. Rev. E 80, 031919 (2009).

45) M. Nicodemi and A. Prisco, “Thermodynamic pathways to genome spatial organization in the cell nucleus”, Biophys. Jour. 96, 2168 (2009).

46) A.Scialdone and M.Nicodemi,“Mechanics and dynamics of X-chromosome pairing at X

14

inactivation”, PLoS Comp. Bio. 5, e10002444 (2008). 47) M. Nicodemi, B. Panning, A. Prisco, “Colocalization transition of homologous chromosomes at

meiosis”, Phys. Rev. E 77, 061913 (2008). 48) M. Nicodemi, B. Panning, A. Prisco, “A thermodynamic switch for chromosome colocalization”,

Genetics 179, 717 (2008). 49) E. Piegari, V. Cataudella, R. Di Maio, L. Milano, M. Nicodemi, and R. Scandone, “A model of

volcanic magma transport by fracturing stress mechanisms”, Geophys. Res. Lett. 35, L06308 (2008).

50) L.deArcangelis,E.Lippiello,C.Godano,M.Nicodemi,“Statistical properties and universality in earthquake and solar flare occurrence”, Eur. Phys. J. B 64, 551 (2008).

51) M. Nicodemi and A. Prisco, “Self-assembly and DNA binding of the blocking factor in X Chromosome Inactivation”, PLoS Comp. Bio. 3, e210 (2007).

52) M.PicaCiamarra, D.deMartino, A.Coniglio, and M.Nicodemi, “Shear and vibration induced order/disorder transitions in granular media”, Eur. Phys. J. E 24, 411 (2007).

53) 81 M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, “Granular packs under vertical tapping: Structure evolu- tion, grain motion, and dynamical heterogeneities”, Phys. Rev. E 75, 021303 (2007).

54) M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, “Phenomenology and theory of horizontally oscillated granular mixtures”, Eur. Phys. J. E 22, 227 (2007).

55) P. D’Angelo, M. Barra, M. Nicodemi, A. Cassinese, “Phase transitions and aging phenomena in dielectric-like polymeric materials investigated by ac measurements”, Jour. Appl. Phys. 101, 044910 (2007).

56) M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, “Dynamically induced effective interaction in periodically driven granular mixtures”, Phys. Rev. Lett. 97, 038001 (2006).

57) M. Pica Ciamarra, M.D. De Vizia, A. Fierro, M. Tarzia, A. Coniglio, M. Nicodemi, “Granular Species Segregation under Vertical Tapping: Effects of Size, Density, Friction, and Shaking Amplitude”, Phys. Rev. Lett. 96, 058001 (2006).

58) L. de Arcangelis, C. Godano, E. Lippiello, M. Nicodemi, “Universality in solar flare and earthquake occur- rence”, Phys. Rev. Lett. 96, 051102 (2006).

59) E. Piegari, V. Cataudella, R. Di Maio, L. Milano, and M. Nicodemi, “A cellular automaton for the factor of safety field in landslides modeling” Geophys. Res. Lett. 33, L01403 (2006).

60) A. Borrelli, I. De Falco, A. Della Cioppa, M. Nicodemi, G. Trautteur, “Performance of Genetic Programming to extract the trend in noisy data series”, Physica A 370, 104 (2006).

61) E. Piegari, V. Cataudella, R. Di Maio, L. Milano, and M. Nicodemi, “Finite driving rate and anisotropy effects in a model for landslides”, Phys. Rev. E 73, 026123 (2006).

62) M. Tarzia, A. Fierro, M. Nicodemi, M. Pica Ciamarra, A. Coniglio, “Size segregation in granular media induced by phase transition”, Phys. Rev. Lett. 95, 078001 (2005).

63) A.Fierro, M. Nicodemi, M. Tarzia, A. de Candia, and A. Coniglio, “Jamming transition in granular media: A mean-field approximation and numerical simulations”, Phys. Rev. E 71, 061305 (2005).

64) M. Pica Ciamarra, A. Coniglio, and M. Nicodemi, “Shear-induced segregation of a granular mixture under horizontal oscillation”, Jour. Phys.: Cond. Matt. 17, S2549 (2005).

65) A.Coniglio, A. Fierro, M. Nicodemi, M. Pica Ciamarra and M. Tarzia, “Statistical mechanics of dense granular media”, Jour. Phys.: Cond. Matt. 17, S2557 (2005).

66) L.P. Oliveira, H.J. Jensen, M. Nicodemi, and P. Sibani, “Record dynamics and the observed temperature plateau in the magnetic-creep rate of type-II superconductors”, Phys. Rev. B 71, 104526 (2005).

67) A. Caiazzo, A. Coniglio, and M. Nicodemi, “Glass glass transition and new dynamical singularity points in an analytically solvable p-spin glass like model”, Phys. Rev. Lett. 93, 215701 (2004).

68) A.Coniglio, A.deCandia, A.Fierro, M.Nicodemi, M.Tarzia, “Statistical mechanics approach to the jamming transition in granular materials”, Physica A 344, 431 (2004).

69) M. Tarzia, A. Fierro, M. Nicodemi, A. Coniglio, “Segregation in fluidized versus tapped packs”, Phys. Rev. Lett. 93, 198002 (2004).

70) M. Nicodemi and H.J. Jensen, “Time dependent phenomena in transport properties and I-V characteristics of a model for driven vortex matter” Jour. Phys.: Cond. Matt. 16, 6789 (2004).

71) M. Tarzia, A. de Candia, A. Fierro, M. Nicodemi, A. Coniglio, “Glass transition in granular media”, Europhys. Lett. 66, 531 (2004).

72) A.Coniglio, A. de Candia, A. Fierro, M. Nicodemi, M. Pica Ciamarra, M. Tarzia, “On Edwards’ theory of powders”, Physica A 339, 1 (2004).

73) A.Coniglio, A. Fierro, M. Nicodemi, “Stationary Probability Distribution in Granular Media”, Physica D 193, 292 (2004).

74) A.Caiazzo, A. Coniglio, and M. Nicodemi, “Phase coexistence and relaxation of the spherical frustrated Blume-Emery-Griffiths model with attractive particles coupling”, Europhys. Lett. 65, 256

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(2004). 75) M. Nicodemi, “The Peak Effect in a driven lattice gas model”, Phys. Rev. E 67, 041103 (2003). 76) A.Fierro, M. Nicodemi, and A. Coniglio, “Edwards’ approach to horizontal and vertical segregation

in a mixture of hard spheres under gravity”, Jour. Phys.: Cond. Matt. 15, 1095 (2003). 77) A.Fierro, M. Nicodemi and A. Coniglio, “Thermodynamic and Statistical Mechanics of frozen

systems in inherent states”, Phys. Rev. E 66, 061301 (2002). 78) S.T.Bramwell,K.Christensen,J.Y.Fortin,P.C.W.Holdsworth,H.J.Jensen,S.Lise,J.Lopez,M.Nicodemi,

J.-F. Pinton, M. Sellitto, “Universal Fluctuations in Correlated Systems” - Reply, Phys. Rev. Lett. 89, 208902 (2002).

79) M. Nicodemi, A. Fierro and A. Coniglio, “Segregation in hard spheres mixtures under gravity. An extension of Edwards approach with two thermodynamical parameters”, Europhys. Lett. 60, 684 (2002).

80) A.Caiazzo, A. Coniglio, and M. Nicodemi, “Dynamics and thermodynamics of the spherical frustrated Blume-Emery-Griffiths model”, Phys. Rev. E 66, 046101 (2002).

81) M. Nicodemi and H.J. Jensen, “Equilibrium and off-equilibrium dynamics in a model for vortices in superconductors”, Phys. Rev. B 65, 144517 (2002).

82) A.Coniglio, A. Fierro, M. Nicodemi, “Probability distribution of inherent states in models of granular media and glasses”, Europ. Jour. Phys. E 9, 219 (2002).

83) D.Hamon,M.NicodemiandH.J.Jensen,“Continuously driven OFC: a simple model of Solar flare statistics”, Astronomy&Astrophysics 387, 326 (2002).

84) A.Fierro,M.Nicodemi,andA.Coniglio,“Equilibrium Distribution of the Inherent States and their Dynamics in Glassy Systems and Granular Media”, Europhys. Lett. 59, 642 (2002).

85) H.J. Jensen and M. Nicodemi, “Memory effects in response functions of driven vortex matter”, Europhys. Lett. 57, 348 (2002).

86) M. Nicodemi and H.J. Jensen, “Nature of temperature independent dissipation and relaxation in layered superconductors” - Reply, Phys. Rev. Lett. 87, 259702 (2001).

87) A.Coniglio,A.Fierro,M.Nicodemi,“Applications of the Statistical Mechanics of Inherent States to Granular Media”, Physica A 302, 193 (2001).

88) M. Nicodemi, “Interplay of dynamical and equilibrium phenomena in vortex matter”, J. Phys.: Cond. Matt. 14, 2403 (2002).

89) S.T.Bramwell,K.Christensen, J.-Y.Fortin, P.C.W.Holdsworth,H.J.Jensen, S.Lise,J.Lopez, M.Nicodemi, J.-F. Pinton, M. Sellitto, “Universal Fluctuations in Correlated Systems” - Reply, Phys. Rev. Lett. 87, 188902 (2001).

90) M.Nicodemi and H.J.Jensen,“Aging and memory phenomena in magnetic and transport properties of vortex matter”, J. Phys. A 34, 8425 (2001).

91) H.J. Jensen and M. Nicodemi, “Off equilibrium properties of vortex creep in superconductors”, Europhys. Lett. 54, 566 (2001).

92) A.Coniglio and M. Nicodemi, “A Statistical Mechanics Approach to the Inherent States of Granular Media”, Physica A 296, 451 (2001).

93) M. Nicodemi, “Vortex matter out of equilibrium”, Fractals 11, 149 (2003). 94) M. Nicodemi and H.J. Jensen, “Off equilibrium magnetic properties in a model of repulsive particles

for vortices in superconductors”, J. Phys. A 34, L11 (2001). 95) F. Corberi, M. Nicodemi, M. Piccioni, A. Coniglio, “Slow dynamics and aging in a constrained

diffusion model”, Phys. Rev. E 63, 031106 (2001). 96) D.K. Jackson, M. Nicodemi, G. Perkins, N. Lindop, H.J. Jensen, “Vortex Clustering: The Origin of

the Second Peak in the Magnetisation Loops of Type Two Superconductors”, Europhys. Lett. 52, 210 (2000).

97) M. Nicodemi and H.J. Jensen, “Second magnetisation peak relaxation in a model for vortices in superconductors”, Physica C 341-348, 1065 (2000).

98) M.Nicodemi,“Domains growth and packing properties in driven granular media subject to gravity”,Physica A 285, 267 (2000).

99) S.T.Bramwell,K.Christensen,J.Y.Fortin,P.C.W.Holdsworth,H.J.Jensen,S.Lise, J.Lopez, M.Nicodemi, J.-F. Pinton, M. Sellitto, “Universal Fluctuations in Correlated Systems”, Phys. Rev. Lett. 84, 3744 (2000).

100) A.Coniglio and M. Nicodemi, “The jamming transition of Granular Media”, Jour. Phys.: Cond. Matt. 12, 6601 (2000).

101) F. Corberi, M. Nicodemi, M. Piccioni, A. Coniglio, “Off-equilibrium dynamics in a singular diffusion model”, Phys. Rev. Lett. 83, 5054 (1999).

102) M. Nicodemi, A. Coniglio, H.J. Herrmann, “Density fluctuations in a model for vibrated granular media”, Phys. Rev. E 59, 6830 (1999).

103) A.Coniglio, E. Caglioti, H.J. Herrmann, V. Loreto, M. Nicodemi, “Cooperative Length and Free-Volume Approach for Granular Media”, Physica A 265, 311 (1999).

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104) A.Coniglio and M. Nicodemi, “Scaling properties in off equilibrium dynamical processes”, Phys. Rev. E 59, 2812 (1999).

105) M.Nicodemi and A. Coniglio, “Aging in out of equilibrium dynamics of models for granular media”, Phys. Rev. Lett. 82, 916 (1999).

106) M.Piccioni,M.Nicodemi,S.Galam,“Logarithmic relaxations in a random-field lattice gas subject to gravity”, Phys. Rev. E 59, 3858 (1999).

107) A.Coniglio, A. de Candia, A. Fierro, M. Nicodemi, “Universality in glassy systems”, Jour. Phys.: Cond. Mat. 11, A167 (1999).

108) H.J. Herrmann, S. Krishnamurthy, V. Loreto, M. Nicodemi, S. Roux, “Internal avalanches in models of granular media”, Fractals 7, 51 (1999).

109) A.Coniglio, E. Caglioti, H.J. Herrmann, V. Loreto, M. Nicodemi, “Segregation of granular mixtures in presence of compaction”, Europhys. Lett. 43, 591 (1998).

110) A.Coniglio, A. de Candia, M. Nicodemi, “Frustration in glass forming liquids and the breakdown of Stokes-Einstein relations”, Il Nuovo Cimento 20D, 2349 (1998).

111) A.Coniglio, E. Caglioti, H.J. Herrmann, V. Loreto, M. Nicodemi, “Geometrical Frustration: a dynamical motor for dry granular media”, Physica A 257, 419 (1998).

112) M. Nicodemi, “A phenomenological theory of dynamic processes in granular media”, Physica A, 257, 448 (1998).

113) M. Nicodemi, “Logarithmic compaction in a 3D model for granular media”, Jour. de Phys. I 7, 1573 (1997).

114) J. Arenzon, M. Nicodemi and M. Sellitto, “The Blume-Emery-Griffiths Spin Glass Model”, Jour. de Phys. I 7, 945 (1997).

115) E.Caglioti,H.J.Herrmann,V.Loreto,M.Nicodemi,“ATetris-like Model for the Compaction of Dry Granular Media”, Phys. Rev. Lett. 79, 1575 (1997).

116) M. Nicodemi and A. Coniglio, “Macroscopic glassy relaxations and microscopic motions in a Frustrated Lattice Gas”, Phys. Rev. E 57, R39 (1998).

117) M. Nicodemi and A. Coniglio, “The glassy transition of the frustrated Ising lattice gas”, J. Phys. A 30, L187 (1997).

118) M. Nicodemi, “Percolation and cluster formalism in continuous spin systems”, Physica A 238, 9 (1997).

119) M. Nicodemi, A. Coniglio, H.J. Herrmann, “Frustration and slow dynamics of granular packings”, Phys.Rev. E 55, 3962 (1997).

120) M. Nicodemi, A. Coniglio, H.J. Herrmann, “Compaction and force propagation in granular packings”, Physica A 240, 405 (1997).

121) M. Nicodemi, A. Coniglio, H.J. Herrmann, “The compaction in granular media and frustrated Ising models”, J. Phys. A 30, L379 (1997).

122) J. Arenzon, M. Nicodemi and M. Sellitto, “Equilibrium properties of the Ising frustrated lattice gas”, Jour. de Phys. I 6, 1143 (1996).

123) V. Cataudella and M. Nicodemi, “Efficient Cluster Dynamics for the Fully Frustrated XY Model”, Physica A 233, 293 (1996).

124) V. Cataudella, G. Franzese, M. Nicodemi, A. Scala and A. Coniglio, “Percolation and cluster Monte Carlo dynamics for spin models”, Phys. Rev. E 54, 175 (1996).

125) M. Nicodemi, “Mapping of frustrated spin systems into percolation models and Monte Carlo cluster dynamics”, Jour. of Phys. A, 29, 1961 (1996).

126) V. Cataudella, G. Franzese, M. Nicodemi, A. Scala, A. Coniglio, “Generalised percolation models and frustrated spin systems”, Il Nuovo Cimento D 16, 1259 (1994).

127) V. Cataudella, G. Franzese, M. Nicodemi, A. Scala, A. Coniglio, “Critical Clusters and Efficient Dynamics for Frustrated Spin Models”, Phys. Rev. Lett. 72, 1541 (1994).

P2. Book contributions

1) M. Nicodemi, “A look at the future” (in Italian), in “Science, Nature, Transformations”, R. Musto, L.M. Sicca, M. Nicodemi Eds., Editoriale Scientifica, IT, 2013.

2) M.Nicodemi,“Self-organization and emergence”, in Lecture Notes in Complexity Science, R.Ball, V.Kolokoltsov, R. MacKay Eds., London Mathematical Society Lecture Note Series: 408 (2013).

3) M. Nicodemi, “Extreme Value Statistics”, in Encyclopedia of Complexity and System Science, R.A. Meyers Ed., Springer, 2009.

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P3. Proceedings 1) A.M.Chiariello, S. Bianco, A. Piccolo, C. Annunziatella, M. Barbieri, A. Pombo, M. Nicodemi (2014)

Polymer models of the organization of chromosomes in the nucleus of cells. Rend. Acc. Sc. Fis. Mat. Napoli, Vol.LXXXI, 2 pp.301-310.

2) E. Piegari, V. Cataudella, R. Di Maio, L. Milano, M. Nicodemi (2007). Un modello statistico per la simulazione di eventi franosi. In: Versace P. LA MITIGAZIONE DEL RISCHIO DA COLATE DI FANGO a Sarno e negli altri Comuni colpiti dagli eventi del maggio 1998. p. 167-173, NAPOLI:COMMGOV2994, Napoli-Sarno, 2-5 maggio 2005

3) E. Piegari, R. Di Maio, G. giordano, P. Capizzi, R. Curciotti, L. Milano, M. Nicodemi (2005). The contribution of electrical resistivity measurements to the analysis of landslide events. In: 11th European Meeting of Environmental and Engineering Geophysics. Palermo (Italy), 4-7 September, 2005, p. B010-1-B010-4, Houten (The Netherlands):EAGE

4) E. Piegari, V. Cataudella, R. Di Maio, L. Milano, M. Nicodemi (2004). Un modello statistico per la valutazione della pericolosità di aree a rischio frana. In: Slejko D., Rebez A.. 23° Convegno Nazionale GNGTS. p. 575-577, TRIESTE:OGS, ISBN: 9788890038587, Roma, 14-16 Dicembre 2004

5) A.Coniglio, M. Nicodemi, M. Pica Ciamarra, A. de Candia, A. Fierro (2003). Statistical Mechanics of Jamming and Segregation in Granular Media. In “Unifying concepts in granular media and glasses”, p. 47-62, Eds. A. Coniglio, A. Fierro, H.J. Herrmann, M. Nicodemi, Elsevier.

P4. Editor

1) “Science, Nature, Transformations” (in Italian), Eds. R. Musto, LM Sicca, M. Nicodemi, (Editoriale Scientifica, IT, 2013).

2) “Granular Matter”, Ed. M. Nicodemi, special issue of Jour. Phys. Cond. Matter, vol.17, n.25, (IoP Publishing U.K., 2005).

3) “Unifying concepts in granular media and glasses”, Eds. A. Coniglio, A. Fierro, H.J. Herrmann, M. Nicodemi, Elsevier Amsterdam, 2004.

MAIN INVITED INTERNATIONAL TALKS (RELAZIONI A CONGRESSI DI RILEVANZA INTERNAZIONALE)

2017, The EMBO Conference: Chromatin and Epigenetics, Heidelberg, DE. 2017, Univ. Paris-1 Panthéon-Sorbonne, Workshop on Topics in Random Geometry, Paris, FR. 2017, McGill Univ. Research Inst., Workshop on The Physical Basis of Functional Genome Organization, CA. 2017, TIGEM Genetics of rare diseases, IT. 2017, Fondazione Pascale, Chromatin architecture and polymer physics, IT. 2016, Humboldt University, IRI for Life Sciences, General Seminar, Berlin, DE. 2016 TEDxCNR, Plenary Talk, Roma, IT. 2016, The EMBO Meeting 2016, Mannheim, DE. 2016, Seminario generale, CNR-ISASI, IT. 2016, TU-Darmstadt, General Seminar, Darmstadt, DE. 2016, Weatherall Institute of Molecular Medicine-MRC, General Seminar, Oxford, UK. 2016, EMS School on Computational Approaches to Chromatin Organization, Bedlewo, Poland. 2016, Int. Conference Genome architecture in space and time, ICTP-Trieste, IT. 2016, Int. Workshop Transcriptional Regulation, Molecular Biotech. Center, Univ. Torino, General Seminar, IT. 2016, Dip.to Medicina Molecolare, Univ. Napoli, PhD General Seminar, IT. 2016, HBS Danube Conference on Epigenetics, Budapest, Hungary. 2016, Dip.to di Biologia, Univ. di Napoli, General Seminar, IT. 2015, IoP Conference on Quantitative Methods in Gene Reg. III, Cambridge, UK. 2015 Int. Workshop&School on Models of Life, NBI Copenhagen, Denmark. 2015, CECAM Workshop Integrating genomics with physical models of DNA and chromosomes, Lyon, FR. 2015, EPIGEN Conf. Long-range interactions in dynamic control of gene expression, IGB-CNR, IT. 2015, Polymer models of chromatin folding, Plenary Talk, Soc.Naz. SS.LL.AA., IT. 2014, Dip.to di Fisica, Sapienza University, Rome, Seminario Generale. 2014, Int. Conf. Chromosome Dynamics: Computational Models and Experimental Data, Royal Society (UK). 2014, Single cell states in stem cell reprogramming, Lecture, Max Delbruck Centrum, Berlin (DE). 2014, Int. Conference Long-Range Genome Organization and Transcription Dynamics, Janelia Res. Campus (USA). 2014, Int. School Chromatin organization: from structure to biological function, EPFL, Crans-Montana, (Swiss). 2013, Int. Workshop Entanglement in biology; how nature controls the topology of DNA, BIRS, Banff, (Canada). 2013, Int. Workshop on Chromosome Structure and Function: Experiments and Modeling, SISSA, Trieste (IT). 2013, Int. Workshop on Monte Carlo Methods: Applications to Polymers and Biological

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Systems, Heidelberg, DE. 2012, European Bioinformatics Institute, Cambridge, UK. 2012, Int. Workshop on Statistical Mechanics, SISSA, IT. 2012, Int. Workshop on Topological Aspects of DNA Function and Protein Folding, Cambridge, UK. 2012, Biozentrum, University of Basel, SW, Colloquium. 2012, Int. Workshop on Imaging the Cell Nucleus, MRC-Imperial College London, UK. 2012, Dip.to di Scienze Biomolecolari e Biotecnologie, CNR-Univ. di Milano, IT Colloquium. 2012, Colloquium, Institute Pasteur, Paris, FR. 2012, Dep.t of Biochem. and Biotech., School of Medicine, Naples, IT, Colloquium. 2011, Dep.t of Biotech. and Biosciences, Università Milano-Bicocca, Milano, IT, Colloquium. 2011, Dip.to di Fisica, Università Roma "La Sapienza", Roma, IT. 2011, Int. Conf. Modeling Life Sciences, Shanghai, China, Keynote Talk. 2011, Convegno Nazionale Fisica Statistica, Parma, IT. 2011, Int. Conf. Computational Biology BiCi, Bertinoro, IT, Plenary Talk. 2010, IRCC, Cancer Research Institute,Torino, Italy 2010,Institute of Mathematical Sciences, Imperial College, London, UK, Colloquium. 2010, Intrnl. Conf. Unwinding Complexity, StatPhys24 Satellite, Port Douglas, AU. 2010, IOP Meeting Complexity and nonlinear phenomena in biological systems, Bath, UK. 2010, Statistical physics of polymers: DNA and proteins, Yukawa Inst. for Theor.Phys., Kyoto University, Japan. 2009, Cambridge IMA Conference on Dense Granular Flows, Newton Institute Cambridge, UK. 2009, PhD School on Complexity in Biology, Torino, Italy, Main Lecturer. 2009, Oxford Condensed Matter Theory Seminar, Oxford UK. 2009, Intrnl. Conf. Methodological challenges for Systems Biology, Venice, Italy. 2009, World Conf. Powders & Grains, Golden, Colorado USA, Plenary Talk. 2009, Dept. of Biochemistry and Biophysics, UCSF San Francisco, USA. 2009, Workshop Computational Approaches to Biology, IGB Napoli, Italy, Keynote Talk. 2009, Intrnl. Workshop Statistical Mechanics of Molecular&Cell Biology, Warwick, UK. 2009, Laboratory of Molecular Biology, MRC, Cambridge, UK. 2008, Centre of System Biology, Warwick Univ., UK. 2008, Int. Conf. Granular gases beyond the dilute limit, Thurnau, Germany. 2008, Int. Conf. of the EU Assoc. of Fluid Mechanics, Manchester, UK. 2008, Int. Workshop Theoretical Approaches for the Genome, Annecy, France. 2007, Univ. di Torino, Italy, "Symmetry Breaking in X Chromosome Inactivation", Colloquium. 2007, UK Condensed Matter Meeting (CMMP), Leicester, UK. 2007, Institute of Mathematics, I.C. London, UK, Colloquium 2007, Dept. of Molecular Biology, Medical School, Harvard University, USA. 2007, Int. Workshop Complex Systems, Canberra, AU, Keynote Talk. 2007, Dept. of Physics, Manchester Univ., UK. 2007, Int. Conf. BioMEMS and Nanotechnology, Canberra, AU, Keynote Talk. 2006, Institut Curie, sect. "Nuclear dynamics and genome plasticity", Paris, France. 2006, Int. Conf. DygraM 2006, Rennes, France, Plenary Talk. 2006, 2nd Int. Conf. "X Chromosome Inactivation", Paris, France. 2006, Int. School/Workshop on "Granular Media", Canberra, Australia, Lectures and Plenary Talk. 2005, Int. Workshop "Granular Matter", I.H.P., Paris, France. 2005, KITP Workshop "Granular Physics", UCSB, Santa Barbara, USA. 2005, Int. Conference "Traffic and Granular Flow 2005", Berlin, Germany, Plenary Talk. 2005, Int. "Econophyiscs Colloquium", Canberra, Australia. 2005, Int. Conf. "Materials and Complexity III", Kioloa, Australia, Keynote Talk. 2005, SPIE Int. Symposium "Complex Systems", Brisbane, Australia, Keynote Talk. 2004, G.M.C.M., Univ. de Rennes, Rennes, France. 2003, "Statistical physics of glassy and non-equilibrium systems" Int. Conf., Villasimius, Italy. 2003, Statistical Mechanics Section King's College, London, U.K. 2003, "Unifying concepts in granular media and glasses", Capri, Italy, Plenary Talk. 2002, Int. Workshop on "Fractal Structures and Self-Organization", Capri, Italy, Keynote Talk. 2002, IPMC EPFL, Lausanne, Switzerland. 2001, Int. Conf. "Scaling Concepts and Complex Systems", Merida, Mexico. 2000, Conference on "Disordered and Complex Systems", King's College, London, U.K. 2000, Condensed Matter Colloquia of Imperial College, London, U.K. 1999, Workshop on "Dynamics of Nonequilibrium Systems", ICTP, Trieste, Italy. 1998, "National Congress of Theoretical and Condensed Matter Physics", Trento, Italy. 1998, "National Congress of I.N.F.M.", Rimini, Italy, Keynote Talk. 1997, "National Congress of Statistical Mechanics", Parma, Italy. 1997, "The Dynamics of Complexity", ICTP, Trieste, Italy. 1997, V Latin American workshop on "Nonlinear Phenomena", Canela, Brazil, Keynote Talk. 1997, Univ. Fed. Rio Grande do Sud, Porto Alegre, Brazil. 1996, Int. Conf. on "Dry Granular Media", Universitè "P. and M. Curie", Paris, France.

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DICHIARAZIONE SOSTITUTIVA DI CERTIFICAZIONI, DI ATTO DI NOTORIETA’ E DI CONFORMITA’ ALL’ORIGINALE DELLE COPIE, AI SENSI DEGLI ARTT. 19, 38, 46 E 47 DEL D.P.R. 445/2000

Il sottoscritto Mario Nicodemi, Codice Fiscale NCDMRA68L30F839Y, nato a Napoli il 30/07/1968, residente in Napoli, Via Orazio 161, 80122, consapevole delle sanzioni penali previste in caso di dichiarazioni non veritiere, falsità negli atti, uso o esibizione di atti falsi o contenenti dati non veritieri, ai sensi dell’art. 76 del D.P.R. 445/2000 e s.m.i.,

DICHIARA

che tutte le informazioni, i documenti, i titoli, le pubblicazioni, presentati ai fini della procedura di valutazione, indicati nel Curriculum Vitae et Studiorum e negli elenchi di titoli e pubblicazioni, e allegati in copia, corrispondono a verità, possono essere certificati e sono conformi agli originali. Dichiara di essere in possesso dei su elencati titoli, documenti e pubblicazioni. Dichiara che in tutti i lavori in collaborazione elencati espressamente nel Curriculum Vitae, e in particolare nelle pubblicazioni presentate ai fini della procedura di valutazione ivi elencate, il proprio contributo individuale è stato determinante e assoluto.

Il sottoscritto acconsente al trattamento dei dati personali e alla pubblicazione dell’elenco dei titoli e delle pubblicazioni scientifiche, degli altri documenti e degli atti relativi alla procedura di valutazione come richiesto nel bando di partecipazione.

Letto, firmato e sottoscritto, con allegata copia del proprio documento di riconoscimento.

Napoli, 15/03/2017

Mario Nicodemi