Modeling approaches toward bioinspired dynamic materials

Project Information

DYNAPOL

Grant agreement ID: 818776

DOI 10.3030/818776

EC signature date 21 December 2018

Start date 1 November 2019

End date 31 October 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 999 623,00

EU contribution € 1 999 623,00

Coordinated by

POLITECNICO DI TORINO
Italy

Publications

Peer reviewed articles (44)

Identifying and Tracking Defects in Dynamic Supramolecular Polymers

Author(s): Piero Gasparotto, Davide Bochicchio, Michele Ceriotti, Giovanni M. Pavan
Published in: The Journal of Physical Chemistry B, Issue 124/3, 2019, Page(s) 589-599, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.9b11015

Swarm-CG : Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Author(s): Charly Empereur-Mot, Luca Pesce, Giovanni Doni, Davide Bochicchio, Riccardo Capelli, Claudio Perego, Giovanni M. Pavan
Published in: ACS Omega, Issue 5/50, 2020, Page(s) 32823-32843, ISSN 2470-1343
Publisher: American Chemical Society
DOI: 10.1021/acsomega.0c05469

Automatic multi-objective optimization of coarse-grained lipid force fields using SwarmCG

Author(s): Charly Empereur-mot, Riccardo Capelli, Mattia Perrone, Cristina Caruso, Giovanni Doni, Giovanni M. Pavan
Published in: The Journal of Chemical Physics, Issue 156, 2022, Page(s) 024801, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0079044

Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization

Author(s): Elisabeth Weyandt, Luigi Leanza, Riccardo Capelli, Giovanni M. Pavan, Ghislaine Vantomme, E. W. Meijer
Published in: Nature Communications, Issue 13, 2022, Page(s) 248, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-27831-2

Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures

Author(s): Aritra Sarkar, Tejmani Behera, Ranjan Sasmal, Riccardo Capelli, Charly Empereur-mot, Jaladhar Mahato, Sarit S. Agasti, Giovanni M. Pavan, Arindam Chowdhury, Subi J. George
Published in: Journal of the American Chemical Society, Issue 142/26, 2020, Page(s) 11528-11539, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c04404

Subtle Stereochemical Effects Influence Binding and Purification Abilities of an Fe^II₄L₄ Cage

Author(s): Xue, Weichao; Pesce, Luca; Bellamkonda, Adinarayana; Ronson, Tanya K.; Wu, Kai; Zhang, Dawei; Vanthuyne, Nicolas; Brotin, Thierry; Martinez, Alexandre; Pavan, Giovanni M.; Nitschke, Jonathan R.
Published in: Journal of the American Chemical Society, Issue 145,9, 2023, Page(s) 5570–5577, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c00294

Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly Polarized Light

Author(s): H. Zhu, L. Pesce, R. Chowdhury, W. Xue, K. Wu, T. K. Ronson, R. H. Friend, G. M. Pavan, J. R. Nitschke
Published in: Journal of the American Chemical Society, Issue 146, 2024, Page(s) 2379–2386, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c11321

Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling

Author(s): Martina Crippa; Annalisa Cardellini; Cristina Caruso; Giovanni M. Pavan
Published in: Proc. Natl. Acad. Sci. USA, Issue 120, 2023, Page(s) e2300565120, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2300565120

Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices

Author(s): C. Lionello, C. Perego, A. Gardin, R. Klajn and G. M. Pavan
Published in: ACS Nano, Issue 17, 2023, Page(s) 275-287, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.2c07558

Molecular communications in complex systems of dynamic supramolecular polymers

Author(s): Martina Crippa, Claudio Perego, Anna L. de Marco, Giovanni M. Pavan
Published in: Nature Communications, Issue 13, 2022, Page(s) 2162, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-29804-5

Controlling Exchange Pathways in Dynamic Supramolecular Polymers by Controlling Defects

Author(s): Anna L. de Marco, Davide Bochicchio, Andrea Gardin, Giovanni Doni, Giovanni M. Pavan
Published in: ACS Nano, Issue 15, 2021, Page(s) 14229–14241, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.1c01398

Non-uniform Photoinduced Unfolding of Supramolecular Polymers Leading to Topological Block Nanofibers

Author(s): Keigo Tashiro, Kosuke Katayama, Kenta Tamaki, Luca Pesce, Nobutaka Shimizu, Hideaki Takagi, Rie Haruki, Martin J. Hollamby, Giovanni M. Pavan, Shiki Yagai
Published in: Angewandte Chemie (International ed.), Issue 60, 2021, Page(s) 26986-26993, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202110224

Biomimetic Synthesis of Sub-20 nm Covalent Organic Frameworks in Water

Author(s): Carlos Franco, David Rodríguez-San-Miguel, Alessandro Sorrenti, Semih Sevim, Ramon Pons, Ana E. Platero-Prats, Marko Pavlovic, Istvan Szilágyi, M. Luisa Ruiz Gonzalez, José M. González-Calbet, Davide Bochicchio, Luca Pesce, Giovanni M. Pavan, Inhar Imaz, Mary Cano-Sarabia, Daniel Maspoch, Salvador Pané, Andrew J. de Mello, Felix Zamora, Josep Puigmartí-Luis
Published in: Journal of the American Chemical Society, Issue 142/7, 2020, Page(s) 3540-3547, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.9b12389

Innate dynamics and identity crisis of a metal surface unveiled by machine learning of atomic environments

Author(s): Matteo Cioni; Daniela Polino; Daniele Rapetti; Luca Pesce; Massimo Delle Piane; Giovanni M. Pavan
Published in: The Journal of Chemical Physics, Issue 158, 2023, Page(s) 124701, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0139010

Multiscale Molecular Modelling of ATP‐Fueled Supramolecular Polymerisation and Depolymerisation**

Author(s): Claudio Perego, Luca Pesce, Riccardo Capelli, Subi J. George, Giovanni M. Pavan
Published in: ChemSystemsChem, Issue 3/2, 2021, ISSN 2570-4206
Publisher: Wiley
DOI: 10.1002/syst.202000038

Systematic exploration of accessible topologies of cage molecules via minimalistic models

Author(s): A. Tarzia, E. H. Wolpert, K. E. Jelfs, G. M. Pavan
Published in: Chemical Science, Issue 14, 2023, Page(s) 12506-12517, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3sc03991a

Into the Dynamics of Rotaxanes at Atomistic Resolution

Author(s): Luigi Leanza; Claudio Perego; Luca Pesce; Matteo Salvalaglio; Max von Delius; Giovanni M. Pavan
Published in: Chemical Science, Issue 14, 2023, Page(s) 6716-6729, ISSN 2041-6520
Publisher: Royal Society of Chemistry

Living supramolecular polymerization of fluorinated cyclohexanes

Author(s): Oleksandr Shyshov, Shyamkumar Vadakket Haridas, Luca Pesce, Haoyuan Qi, Andrea Gardin, Davide Bochicchio, Ute Kaiser, Giovanni M. Pavan, Max von Delius
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-23370-y

Porous covalent organic nanotubes and their assembly in loops and toroids

Author(s): Kalipada Koner; Shayan Karak; Sharath Kandambeth; Suvendu Karak; Neethu Thomas; Luigi Leanza; Claudio Perego; Luca Pesce; Riccardo Capelli; Monika Moun; Monika Bhakar; Thalasseril G. Ajithkumar; Giovanni M. Pavan; Rahul Banerjee
Published in: Nature Chemistry, Issue 14, 2022, Page(s) 507-514, ISSN 1755-4330
Publisher: Nature Publishing Group
DOI: 10.1038/s41557-022-00908-1

Lessons Learned from Multiobjective Automatic Optimizations of Classical Three-Site Rigid Water Models Using Microscopic and Macroscopic Target Experimental Observables

Author(s): M. Perrone, R. Capelli, C. Empereur-mot, A. Hassanali, G. M. Pavan
Published in: Journal of Chemical & Engineering Data, Issue 68, 2023, Page(s) 3228–3241, ISSN 0021-9568
Publisher: American Chemical Society
DOI: 10.1021/acs.jced.3c00538

Understanding functional group and assembly dynamics in temperature responsive systems leads to design principles for enzyme responsive assemblies.

Author(s): Hongxu Liu; Chiara Lionello; Jenna Westley; Annalisa Cardellini; Uyen Huynh; Giovanni M. Pavan; Sankaran Thayumanavan
Published in: Nanoscale, Issue 13, 2021, Page(s) 11568-11575, ISSN 2040-3372
Publisher: Royal Society of Chemistry
DOI: 10.1039/d1nr02000e

Synthesis of C60/[10]CPP-catenanes by regioselective, nanocapsule-templated bingel bis-addition

Author(s): F. M. Steudel, E. Ubasart, L. Leanza, M. Pujals, T. Parella, G. M. Pavan, X. Ribas, M. von Delius
Published in: Angew. Chem. Int. Ed., Issue 62,42, 2023, Page(s) e202309393, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202309393

Ephemeral ice-like local environments in classical rigid models of liquid water

Author(s): R. Capelli, F. Muniz-Miranda, G. M. Pavan
Published in: The Journal of Chemical Physics, Issue 156, 2022, Page(s) 214503, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0088599

Solvent-driven chirality for luminescent self-assembled structures: experiments and theory

Author(s): Charles Lochenie, Alberto Insuasty, Tommaso Battisti, Luca Pesce, Andrea Gardin, Claudio Perego, Mike Dentinger, Di Wang, Giovanni M. Pavan, Alessandro Aliprandi, Luisa De Cola
Published in: Nanoscale, Issue 12/41, 2020, Page(s) 21359-21367, ISSN 2040-3364
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0nr04524a

Well-Tempered Metadynamics Simulations Predict the Structural and Dynamic Properties of a Chiral 24-Atom Macrocycle in Solution

Author(s): R. Capelli, A. J. Menke, H. Pan, B. G. Janesko, E. E. Simanek, G. M. Pavan
Published in: ACS Omega, Issue 7/34, 2022, Page(s) 30291–30296, ISSN 2470-1343
Publisher: American Chemical Society
DOI: 10.1021/acsomega.2c03536

Machine learning of microscopic structure-dynamics relationships in complex molecular systems

Author(s): M. Crippa, A. Cardellini, M. Cioni, G. Csányi, G. M. Pavan
Published in: Machine Learning: Science and Technology, Issue 4, 2023, Page(s) 045044, ISSN 2632-2153
Publisher: Institute of Physics Publishing
DOI: 10.1088/2632-2153/ad0fa5

Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage

Author(s): Luca Pesce, Claudio Perego, Angela B. Grommet, Rafal Klajn, Giovanni M. Pavan
Published in: Journal of the American Chemical Society, Issue 142/21, 2020, Page(s) 9792-9802, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c03444

Classifying soft self-assembled materials via unsupervised machine learning of defects

Author(s): A. Gardin, C. Perego, G. Doni, G. M. Pavan
Published in: Communications Chemistry, Issue 5, 2022, Page(s) 82, ISSN 2399-3669
Publisher: Springer Nature
DOI: 10.1038/s42004-022-00699-z

Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures

Author(s): Tong Bian, Andrea Gardin, Julius Gemen, Lothar Houben, Claudio Perego, Byeongdu Lee, Nadav Elad, Zonglin Chu, Giovanni M. Pavan, Rafal Klajn
Published in: Nature Chemistry, Issue 13, 2021, Page(s) 940–949, ISSN 1755-4330
Publisher: Nature Publishing Group
DOI: 10.1038/s41557-021-00752-9

Reconstructing reactivity in dynamic host–guest systems at atomistic resolution: amide hydrolysis under confinement in the cavity of a coordination cage

Author(s): M. Delle Piane, L. Pesce, M. Cioni, G. M. Pavan
Published in: Chemical Science, Issue 13, 2022, Page(s) 11232-11245, ISSN 2041-6539
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2sc02000a

Solvent-Driven Supramolecular Wrapping of Self-Assembled Structures

Author(s): Guillermo Moreno-Alcántar, Alessandro Aliprandi, Remi Rouquette, Luca Pesce, Klaus Wurst, Claudio Perego, Peter Brüggeller, Giovanni M. Pavan, Luisa De Cola
Published in: Angewandte Chemie. International Edition, Issue 10, 2021, Page(s) 5407-5413, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202013474

Self-assembled poly-catenanes from supramolecular toroidal building blocks

Author(s): Sougata Datta, Yasuki Kato, Seiya Higashiharaguchi, Keisuke Aratsu, Atsushi Isobe, Takuho Saito, Deepak D. Prabhu, Yuichi Kitamoto, Martin J. Hollamby, Andrew J. Smith, Robert Dalgliesh, Najet Mahmoudi, Luca Pesce, Claudio Perego, Giovanni M. Pavan, Shiki Yagai
Published in: Nature, Issue 583/7816, 2020, Page(s) 400-405, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2445-z

Improving Fatigue Resistance of Dihydropyrene by Encapsulation within a Coordination Cage

Author(s): Martina Canton, Angela B. Grommet, Luca Pesce, Julius Gemen, Shiming Li, Yael Diskin-Posner, Alberto Credi, Giovanni M. Pavan, Joakim Andréasson, Rafal Klajn
Published in: Journal of the American Chemical Society, Issue 142/34, 2020, Page(s) 14557-14565, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c06146

A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields

Author(s): Riccardo Capelli, Andrea Gardin, Charly Empereur-mot, Giovanni Doni, Giovanni M. Pavan
Published in: The Journal of Physical Chemistry B, Issue 125, 2021, Page(s) 7785-7796, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.1c02503

Exploring the Potential of Benzene-1,3,5-tricarboxamide Supramolecular Polymers as Biomaterials

Author(s): Silvia Varela-Aramburu, Giulia Morgese, Lu Su, Sandra M. C. Schoenmakers, Mattia Perrone, Luigi Leanza, Claudio Perego, Giovanni M. Pavan, Anja R. A. Palmans, E. W. Meijer
Published in: Biomacromolecules, Issue 21/10, 2020, Page(s) 4105-4115, ISSN 1525-7797
Publisher: American Chemical Society
DOI: 10.1021/acs.biomac.0c00904

Machine learning of atomic dynamics and statistical surface identities in gold nanoparticles

Author(s): Daniele Rapetti; Massimo Delle Piane; Matteo Cioni; Daniela Polino; Riccardo Ferrando; Giovanni M. Pavan
Published in: Communications Chemistry, Issue 6, 2023, Page(s) 143, ISSN 2399-3669
Publisher: Springer Nature
DOI: 10.1038/s42004-023-00936-z

Automatic optimization of lipid models in the Martini force field using SwarmCG

Author(s): C. Empereur-mot, K. B. Pedersen, R. Capelli, M. Crippa, C. Caruso, M. Perrone, P. C. T. Souza, S. J. Marrink, G. M. Pavan
Published in: J. Chem. Inf. Model., Issue 63, 2023, Page(s) 3827–3838, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.3c00530

Toward Chemotactic Supramolecular Nanoparticles: From Autonomous Surface Motion Following Specific Chemical Gradients to Multivalency-Controlled Disassembly

Author(s): Chiara Lionello, Andrea Gardin, Annalisa Cardellini, Davide Bochicchio, Manisha Shivrayan, Ann Fernandez, S. Thayumanavan, Giovanni M. Pavan
Published in: ACS Nano, Issue 15, 2021, Page(s) 16149–16161, ISSN 1936-0851
Publisher: American Chemical Society
DOI: 10.1021/acsnano.1c05000

Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles

Author(s): Annalisa Cardellini; Martina Crippa; Chiara Lionello; Syed Pavel Afrose; Dibyendu Das; Giovanni M. Pavan
Published in: The Journal of Physical Chemistry B, Issue 127,11, 2023, Page(s) 2595–2608, ISSN 1520-6106
Publisher: American Chemical Society

Discordant Supramolecular Fibres Reversibly Depolymerised by Temperature and Light

Author(s): Marieke Gerth, José Augusto Berrocal, Davide Bochicchio, Giovanni M. Pavan, Ilja K. Voets
Published in: Chemistry – A European Journal, Issue 27/5, 2021, Page(s) 1829-1838, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202004115

TimeSOAP: tracking high-dimensional fluctuations in complex molecular systems via time-variations of SOAP spectra

Author(s): C. Caruso, A. Cardellini, M. Crippa, D. Rapetti, G. M. Pavan
Published in: J. Chem. Phys., Issue 158, 2023, Page(s) 214302, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0147025

Self-Sorted, Random, and Block Supramolecular Copolymers via Sequence Controlled, Multicomponent Self-Assembly

Author(s): Aritra Sarkar, Ranjan Sasmal, Charly Empereur-mot, Davide Bochicchio, Srinath V. K. Kompella, Kamna Sharma, Shikha Dhiman, Balasubramanian Sundaram, Sarit S. Agasti, Giovanni M. Pavan, Subi J. George
Published in: Journal of the American Chemical Society, Issue 142/16, 2020, Page(s) 7606-7617, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.0c01822

Reconstitution of microtubule into GTP-responsive nanocapsules

Author(s): N. Uchida, A. Kohata, K. Okuro, A. Cardellini, C. Lionello, E. A. Zizzi, M. A. Deriu, G. M. Pavan, M. Tomishige, T. Hikima, T. Aida
Published in: Nature Communications, Issue 13, 2022, Page(s) 5424, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-33156-5

Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges

Author(s): I. Insua, A. Cardellini, S. Díaz, J. Bergueiro, R. Capelli, G. M. Pavan, J. Montenegro
Published in: Chemical Science, Issue 14, 2023, Page(s) 14074-14081, ISSN 2041-6520
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3sc03930g